Starting phenix.real_space_refine (version: dev) on Sun Feb 19 05:51:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/02_2023/7qey_13944_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/02_2023/7qey_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_13944/02_2023/7qey_13944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/02_2023/7qey_13944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/02_2023/7qey_13944_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/02_2023/7qey_13944_updated.pdb" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 50 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: 50 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: 50 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: 50 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: 50 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: 50 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: 6.08, per 1000 atoms: 0.64 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: 3.98 Conformation dependent library (CDL) restraints added in 1.3 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: 0.87 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: 2.59 Time building geometry restraints manager: 4.30 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=" C7 LMT G 305 " pdb=" C8 LMT G 305 " ideal model delta sigma weight residual 1.489 1.569 -0.080 2.50e-02 1.60e+03 1.01e+01 bond pdb=" C7 LMT K 304 " pdb=" C8 LMT K 304 " ideal model delta sigma weight residual 1.489 1.569 -0.080 2.50e-02 1.60e+03 1.01e+01 bond pdb=" C7 LMT L 304 " pdb=" C8 LMT L 304 " ideal model delta sigma weight residual 1.489 1.568 -0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" C7 LMT J 305 " pdb=" C8 LMT J 305 " ideal model delta sigma weight residual 1.489 1.568 -0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" C7 LMT J 304 " pdb=" C8 LMT J 304 " ideal model delta sigma weight residual 1.489 1.568 -0.079 2.50e-02 1.60e+03 1.01e+01 ... (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=" C1 LMT G 303 " pdb=" C2 LMT G 303 " pdb=" C3 LMT G 303 " ideal model delta sigma weight residual 116.40 109.50 6.90 2.18e+00 2.10e-01 1.00e+01 angle pdb=" C1 LMT I 305 " pdb=" C2 LMT I 305 " pdb=" C3 LMT I 305 " ideal model delta sigma weight residual 116.40 109.51 6.89 2.18e+00 2.10e-01 9.99e+00 angle pdb=" C1 LMT H 303 " pdb=" C2 LMT H 303 " pdb=" C3 LMT H 303 " ideal model delta sigma weight residual 116.40 109.51 6.89 2.18e+00 2.10e-01 9.98e+00 angle pdb=" C1 LMT K 305 " pdb=" C2 LMT K 305 " pdb=" C3 LMT K 305 " ideal model delta sigma weight residual 116.40 109.52 6.88 2.18e+00 2.10e-01 9.95e+00 angle pdb=" C1 LMT G 305 " pdb=" C2 LMT G 305 " pdb=" C3 LMT G 305 " ideal model delta sigma weight residual 116.40 109.53 6.87 2.18e+00 2.10e-01 9.93e+00 ... (remaining 12685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.23: 4902 11.23 - 22.46: 384 22.46 - 33.69: 102 33.69 - 44.93: 60 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 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. 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: 5.630 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: 18.400 Check model and map are aligned: 0.150 Process input model: 27.540 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 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 : 0.009 0.080 9414 Z= 0.572 Angle : 0.572 6.903 12690 Z= 0.280 Chirality : 0.035 0.103 1422 Planarity : 0.003 0.023 1500 Dihedral : 10.736 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 % 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 *********************** 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 : 1.111 Fit side-chains outliers start: 23 outliers final: 5 residues processed: 240 average time/residue: 0.8916 time to fit residues: 234.2085 Evaluate side-chains 172 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 167 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.3810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 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: 0.6980 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: 0.7782 ------------------------------------------------------------------------------- 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: 0.9035 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 9414 Z= 0.235 Angle : 0.636 10.359 12690 Z= 0.332 Chirality : 0.043 0.129 1422 Planarity : 0.003 0.019 1500 Dihedral : 8.686 57.679 1362 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 2.97 % 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: 2.98 (0.25), residues: 1068 helix: 2.85 (0.17), residues: 738 sheet: 3.25 (0.61), residues: 66 loop : -1.10 (0.35), residues: 264 *********************** 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: 29 poor density : 190 time to evaluate : 1.168 Fit side-chains outliers start: 29 outliers final: 16 residues processed: 202 average time/residue: 0.9812 time to fit residues: 215.7928 Evaluate side-chains 188 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 8 residues processed: 8 average time/residue: 0.1266 time to fit residues: 2.9539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 81 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 78 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.9041 moved from start: 0.2349 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= 0.225 Angle : 0.602 7.713 12690 Z= 0.309 Chirality : 0.042 0.146 1422 Planarity : 0.003 0.050 1500 Dihedral : 8.413 59.932 1362 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 3.37 % 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: 3.23 (0.18), residues: 732 sheet: 2.67 (0.56), residues: 66 loop : -1.27 (0.35), residues: 270 *********************** 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 217 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 184 time to evaluate : 1.111 Fit side-chains outliers start: 33 outliers final: 18 residues processed: 195 average time/residue: 0.9832 time to fit residues: 208.5647 Evaluate side-chains 191 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 7 residues processed: 12 average time/residue: 0.4983 time to fit residues: 8.3646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.7980 chunk 73 optimal weight: 0.0070 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 51 optimal weight: 0.0980 chunk 93 optimal weight: 0.0570 chunk 28 optimal weight: 0.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- 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: 0.9011 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 9414 Z= 0.158 Angle : 0.567 9.368 12690 Z= 0.283 Chirality : 0.040 0.132 1422 Planarity : 0.002 0.020 1500 Dihedral : 7.899 59.769 1362 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 2.35 % 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: 3.37 (0.26), residues: 1068 helix: 3.26 (0.18), residues: 738 sheet: 2.81 (0.56), residues: 66 loop : -1.21 (0.35), residues: 264 *********************** 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 207 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 184 time to evaluate : 1.202 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 193 average time/residue: 0.9118 time to fit residues: 192.6651 Evaluate side-chains 186 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.356 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 8 average time/residue: 0.3140 time to fit residues: 4.8035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.1980 chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 0.0870 chunk 26 optimal weight: 4.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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: 0.9013 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9414 Z= 0.169 Angle : 0.560 9.283 12690 Z= 0.282 Chirality : 0.040 0.151 1422 Planarity : 0.002 0.016 1500 Dihedral : 7.684 59.858 1362 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 2.66 % 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: 3.38 (0.25), residues: 1068 helix: 3.29 (0.18), residues: 738 sheet: 2.79 (0.55), residues: 66 loop : -1.25 (0.35), residues: 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 178 time to evaluate : 1.032 Fit side-chains outliers start: 26 outliers final: 16 residues processed: 185 average time/residue: 0.9284 time to fit residues: 187.7542 Evaluate side-chains 189 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 173 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 7 residues processed: 12 average time/residue: 0.3820 time to fit residues: 6.9296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 5.9990 chunk 94 optimal weight: 0.0010 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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: 0.9034 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9414 Z= 0.202 Angle : 0.586 8.900 12690 Z= 0.297 Chirality : 0.042 0.138 1422 Planarity : 0.002 0.017 1500 Dihedral : 7.579 59.818 1362 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 3.48 % 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: 3.31 (0.25), residues: 1068 helix: 3.23 (0.18), residues: 738 sheet: 2.59 (0.55), residues: 66 loop : -1.22 (0.35), residues: 264 *********************** 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 210 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 1.088 Fit side-chains outliers start: 34 outliers final: 17 residues processed: 191 average time/residue: 0.9301 time to fit residues: 193.6737 Evaluate side-chains 184 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 10 residues processed: 11 average time/residue: 0.3201 time to fit residues: 5.6411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 0.0060 chunk 48 optimal weight: 0.0030 chunk 64 optimal weight: 0.6980 overall best weight: 0.3406 ------------------------------------------------------------------------------- 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: 0.9012 moved from start: 0.2832 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= 0.163 Angle : 0.587 8.984 12690 Z= 0.295 Chirality : 0.040 0.152 1422 Planarity : 0.002 0.017 1500 Dihedral : 7.271 59.655 1362 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 2.35 % 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: 3.34 (0.26), residues: 1068 helix: 3.25 (0.18), residues: 738 sheet: 2.77 (0.56), residues: 66 loop : -1.27 (0.35), residues: 264 *********************** 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: 23 poor density : 171 time to evaluate : 1.084 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 179 average time/residue: 1.0451 time to fit residues: 204.6431 Evaluate side-chains 182 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 170 time to evaluate : 1.203 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 4 residues processed: 12 average time/residue: 0.1877 time to fit residues: 4.5597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 31 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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: 0.9027 moved from start: 0.2918 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= 0.198 Angle : 0.613 8.940 12690 Z= 0.308 Chirality : 0.042 0.186 1422 Planarity : 0.002 0.018 1500 Dihedral : 7.060 58.524 1362 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 1.74 % 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: 3.20 (0.18), residues: 738 sheet: 2.62 (0.55), residues: 66 loop : -1.24 (0.35), residues: 264 *********************** 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 188 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 0.905 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 178 average time/residue: 0.8913 time to fit residues: 173.7055 Evaluate side-chains 180 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 8 average time/residue: 0.2734 time to fit residues: 4.5691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.3980 chunk 97 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.9031 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9414 Z= 0.209 Angle : 0.637 9.299 12690 Z= 0.317 Chirality : 0.043 0.220 1422 Planarity : 0.002 0.017 1500 Dihedral : 6.807 56.092 1362 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 1.94 % 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: 3.22 (0.25), residues: 1068 helix: 3.15 (0.18), residues: 738 sheet: 2.53 (0.55), residues: 66 loop : -1.22 (0.35), residues: 264 *********************** 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: 19 poor density : 168 time to evaluate : 1.081 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 174 average time/residue: 0.9277 time to fit residues: 176.2294 Evaluate side-chains 175 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 10 average time/residue: 0.5239 time to fit residues: 7.4370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 0.1980 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.9026 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9414 Z= 0.195 Angle : 0.639 9.667 12690 Z= 0.315 Chirality : 0.042 0.259 1422 Planarity : 0.002 0.016 1500 Dihedral : 6.445 57.038 1362 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 1.12 % 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: 3.20 (0.25), residues: 1068 helix: 3.13 (0.18), residues: 738 sheet: 2.62 (0.55), residues: 66 loop : -1.24 (0.35), residues: 264 ********************** 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 178 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 1.262 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 171 average time/residue: 0.9244 time to fit residues: 172.7789 Evaluate side-chains 175 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 166 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 7 average time/residue: 0.2395 time to fit residues: 3.6114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.126419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.080655 restraints weight = 12427.115| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.60 r_work: 0.2827 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9255 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 9414 Z= 0.230 Angle : 0.659 9.596 12690 Z= 0.327 Chirality : 0.044 0.273 1422 Planarity : 0.003 0.017 1500 Dihedral : 6.334 57.241 1362 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 1.23 % 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: 3.13 (0.25), residues: 1068 helix: 3.09 (0.18), residues: 738 sheet: 2.46 (0.54), residues: 66 loop : -1.24 (0.35), residues: 264 =============================================================================== Job complete usr+sys time: 4198.78 seconds wall clock time: 75 minutes 42.68 seconds (4542.68 seconds total)