Starting phenix.real_space_refine on Sun Apr 7 23:31:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgs_40466/04_2024/8sgs_40466_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgs_40466/04_2024/8sgs_40466.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgs_40466/04_2024/8sgs_40466_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgs_40466/04_2024/8sgs_40466_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgs_40466/04_2024/8sgs_40466_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgs_40466/04_2024/8sgs_40466.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgs_40466/04_2024/8sgs_40466.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgs_40466/04_2024/8sgs_40466_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgs_40466/04_2024/8sgs_40466_trim_updated.pdb" } resolution = 3.15 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= 0.002 sd= 0.013 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: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 80 5.16 5 C 7364 2.51 5 N 2000 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11720 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2829 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 365} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2829 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 365} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2829 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 365} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2829 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 365} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.35, per 1000 atoms: 0.54 Number of scatterers: 11720 At special positions: 0 Unit cell: (96.5835, 99.8855, 94.9325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 20 15.00 O 2256 8.00 N 2000 7.00 C 7364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.76 Conformation dependent library (CDL) restraints added in 2.2 seconds 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 12 sheets defined 57.0% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 36 through 63 removed outlier: 4.979A pdb=" N PHE A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Proline residue: A 55 - end of helix removed outlier: 4.886A pdb=" N ALA A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLN A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 95 through 108 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 141 through 144 No H-bonds generated for 'chain 'A' and resid 141 through 144' Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 260 through 296 Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 308 through 336 Processing helix chain 'A' and resid 342 through 367 Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 378 through 389 removed outlier: 4.058A pdb=" N ILE A 387 " --> pdb=" O ARG A 383 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 410 Processing helix chain 'B' and resid 36 through 63 removed outlier: 4.979A pdb=" N PHE B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Proline residue: B 55 - end of helix removed outlier: 4.886A pdb=" N ALA B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLN B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 77 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 95 through 108 Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 124 through 130 Processing helix chain 'B' and resid 133 through 139 Processing helix chain 'B' and resid 141 through 144 No H-bonds generated for 'chain 'B' and resid 141 through 144' Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 260 through 296 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 308 through 336 Processing helix chain 'B' and resid 342 through 367 Processing helix chain 'B' and resid 369 through 372 No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 378 through 389 removed outlier: 4.058A pdb=" N ILE B 387 " --> pdb=" O ARG B 383 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'C' and resid 36 through 63 removed outlier: 4.979A pdb=" N PHE C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Proline residue: C 55 - end of helix removed outlier: 4.886A pdb=" N ALA C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLN C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 77 Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 95 through 108 Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 124 through 130 Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 141 through 144 No H-bonds generated for 'chain 'C' and resid 141 through 144' Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 260 through 296 Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 308 through 336 Processing helix chain 'C' and resid 342 through 367 Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 378 through 389 removed outlier: 4.059A pdb=" N ILE C 387 " --> pdb=" O ARG C 383 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR C 388 " --> pdb=" O ASP C 384 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 410 Processing helix chain 'D' and resid 36 through 63 removed outlier: 4.980A pdb=" N PHE D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Proline residue: D 55 - end of helix removed outlier: 4.887A pdb=" N ALA D 58 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLN D 59 " --> pdb=" O PRO D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 77 Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 95 through 108 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 124 through 130 Processing helix chain 'D' and resid 133 through 139 Processing helix chain 'D' and resid 141 through 144 No H-bonds generated for 'chain 'D' and resid 141 through 144' Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 260 through 296 Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 308 through 336 Processing helix chain 'D' and resid 342 through 367 Processing helix chain 'D' and resid 369 through 372 No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 378 through 389 removed outlier: 4.058A pdb=" N ILE D 387 " --> pdb=" O ARG D 383 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR D 388 " --> pdb=" O ASP D 384 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU D 389 " --> pdb=" O ALA D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 410 Processing sheet with id= A, first strand: chain 'A' and resid 169 through 171 Processing sheet with id= B, first strand: chain 'A' and resid 194 through 200 Processing sheet with id= C, first strand: chain 'A' and resid 222 through 224 Processing sheet with id= D, first strand: chain 'B' and resid 169 through 171 Processing sheet with id= E, first strand: chain 'B' and resid 194 through 200 Processing sheet with id= F, first strand: chain 'B' and resid 222 through 224 Processing sheet with id= G, first strand: chain 'C' and resid 169 through 171 Processing sheet with id= H, first strand: chain 'C' and resid 194 through 200 Processing sheet with id= I, first strand: chain 'C' and resid 222 through 224 Processing sheet with id= J, first strand: chain 'D' and resid 169 through 171 Processing sheet with id= K, first strand: chain 'D' and resid 194 through 200 Processing sheet with id= L, first strand: chain 'D' and resid 222 through 224 640 hydrogen bonds defined for protein. 1896 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: 3.40 Time building geometry restraints manager: 5.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.78: 11800 1.78 - 2.35: 140 2.35 - 2.91: 0 2.91 - 3.48: 0 3.48 - 4.05: 8 Bond restraints: 11948 Sorted by residual: bond pdb=" AP1 COA B1002 " pdb="AO5* COA B1002 " ideal model delta sigma weight residual 1.610 4.047 -2.437 2.00e-02 2.50e+03 1.48e+04 bond pdb=" AP1 COA D1002 " pdb="AO5* COA D1002 " ideal model delta sigma weight residual 1.610 4.046 -2.436 2.00e-02 2.50e+03 1.48e+04 bond pdb=" AP1 COA A1002 " pdb="AO5* COA A1002 " ideal model delta sigma weight residual 1.610 4.046 -2.436 2.00e-02 2.50e+03 1.48e+04 bond pdb=" AP1 COA C1002 " pdb="AO5* COA C1002 " ideal model delta sigma weight residual 1.610 4.046 -2.436 2.00e-02 2.50e+03 1.48e+04 bond pdb=" AO6 COA D1002 " pdb=" AP2 COA D1002 " ideal model delta sigma weight residual 1.610 3.914 -2.304 2.00e-02 2.50e+03 1.33e+04 ... (remaining 11943 not shown) Histogram of bond angle deviations from ideal: 31.50 - 57.51: 8 57.51 - 83.52: 4 83.52 - 109.53: 1096 109.53 - 135.55: 15124 135.55 - 161.56: 12 Bond angle restraints: 16244 Sorted by residual: angle pdb=" C7 FAD D1001 " pdb=" C8 FAD D1001 " pdb=" C8M FAD D1001 " ideal model delta sigma weight residual 43.09 121.02 -77.93 3.00e+00 1.11e-01 6.75e+02 angle pdb=" C7 FAD B1001 " pdb=" C8 FAD B1001 " pdb=" C8M FAD B1001 " ideal model delta sigma weight residual 43.09 121.01 -77.92 3.00e+00 1.11e-01 6.75e+02 angle pdb=" C7 FAD A1001 " pdb=" C8 FAD A1001 " pdb=" C8M FAD A1001 " ideal model delta sigma weight residual 43.09 121.01 -77.92 3.00e+00 1.11e-01 6.75e+02 angle pdb=" C7 FAD C1001 " pdb=" C8 FAD C1001 " pdb=" C8M FAD C1001 " ideal model delta sigma weight residual 43.09 120.97 -77.88 3.00e+00 1.11e-01 6.74e+02 angle pdb=" AO3 COA C1002 " pdb=" AP1 COA C1002 " pdb="AO5* COA C1002 " ideal model delta sigma weight residual 102.60 31.50 71.10 3.00e+00 1.11e-01 5.62e+02 ... (remaining 16239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 6996 34.08 - 68.16: 144 68.16 - 102.24: 20 102.24 - 136.31: 8 136.31 - 170.39: 4 Dihedral angle restraints: 7172 sinusoidal: 2844 harmonic: 4328 Sorted by residual: dihedral pdb=" AO3 COA C1002 " pdb=" AP1 COA C1002 " pdb="AO5* COA C1002 " pdb="AC5* COA C1002 " ideal model delta sinusoidal sigma weight residual -68.06 102.33 -170.39 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" AO3 COA B1002 " pdb=" AP1 COA B1002 " pdb="AO5* COA B1002 " pdb="AC5* COA B1002 " ideal model delta sinusoidal sigma weight residual -68.06 102.32 -170.38 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" AO3 COA A1002 " pdb=" AP1 COA A1002 " pdb="AO5* COA A1002 " pdb="AC5* COA A1002 " ideal model delta sinusoidal sigma weight residual -68.06 102.20 -170.26 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 7169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1700 0.080 - 0.160: 96 0.160 - 0.241: 4 0.241 - 0.321: 0 0.321 - 0.401: 4 Chirality restraints: 1804 Sorted by residual: chirality pdb="AC2* COA C1002 " pdb="AC1* COA C1002 " pdb="AC3* COA C1002 " pdb="AO2* COA C1002 " both_signs ideal model delta sigma weight residual False -2.47 -2.87 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb="AC2* COA A1002 " pdb="AC1* COA A1002 " pdb="AC3* COA A1002 " pdb="AO2* COA A1002 " both_signs ideal model delta sigma weight residual False -2.47 -2.87 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb="AC2* COA D1002 " pdb="AC1* COA D1002 " pdb="AC3* COA D1002 " pdb="AO2* COA D1002 " both_signs ideal model delta sigma weight residual False -2.47 -2.87 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 1801 not shown) Planarity restraints: 2036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1B FAD C1001 " 0.414 2.00e-02 2.50e+03 5.23e-01 6.16e+03 pdb=" C2B FAD C1001 " -0.620 2.00e-02 2.50e+03 pdb=" C3B FAD C1001 " -0.250 2.00e-02 2.50e+03 pdb=" C4B FAD C1001 " 0.240 2.00e-02 2.50e+03 pdb=" C5B FAD C1001 " -0.750 2.00e-02 2.50e+03 pdb=" N9A FAD C1001 " -0.026 2.00e-02 2.50e+03 pdb=" O2B FAD C1001 " -0.440 2.00e-02 2.50e+03 pdb=" O3B FAD C1001 " 0.783 2.00e-02 2.50e+03 pdb=" O4B FAD C1001 " 0.647 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B FAD A1001 " 0.415 2.00e-02 2.50e+03 5.23e-01 6.16e+03 pdb=" C2B FAD A1001 " -0.619 2.00e-02 2.50e+03 pdb=" C3B FAD A1001 " -0.250 2.00e-02 2.50e+03 pdb=" C4B FAD A1001 " 0.240 2.00e-02 2.50e+03 pdb=" C5B FAD A1001 " -0.750 2.00e-02 2.50e+03 pdb=" N9A FAD A1001 " -0.026 2.00e-02 2.50e+03 pdb=" O2B FAD A1001 " -0.440 2.00e-02 2.50e+03 pdb=" O3B FAD A1001 " 0.783 2.00e-02 2.50e+03 pdb=" O4B FAD A1001 " 0.646 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B FAD B1001 " -0.415 2.00e-02 2.50e+03 5.23e-01 6.16e+03 pdb=" C2B FAD B1001 " 0.620 2.00e-02 2.50e+03 pdb=" C3B FAD B1001 " 0.249 2.00e-02 2.50e+03 pdb=" C4B FAD B1001 " -0.240 2.00e-02 2.50e+03 pdb=" C5B FAD B1001 " 0.750 2.00e-02 2.50e+03 pdb=" N9A FAD B1001 " 0.026 2.00e-02 2.50e+03 pdb=" O2B FAD B1001 " 0.440 2.00e-02 2.50e+03 pdb=" O3B FAD B1001 " -0.783 2.00e-02 2.50e+03 pdb=" O4B FAD B1001 " -0.647 2.00e-02 2.50e+03 ... (remaining 2033 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 25 2.37 - 3.00: 6405 3.00 - 3.63: 18540 3.63 - 4.27: 28064 4.27 - 4.90: 47012 Nonbonded interactions: 100046 Sorted by model distance: nonbonded pdb=" AP2 COA C1002 " pdb="AO5* COA C1002 " model vdw 1.737 2.720 nonbonded pdb=" AP2 COA A1002 " pdb="AO5* COA A1002 " model vdw 1.738 2.720 nonbonded pdb=" AP2 COA D1002 " pdb="AO5* COA D1002 " model vdw 1.738 2.720 nonbonded pdb=" AP2 COA B1002 " pdb="AO5* COA B1002 " model vdw 1.738 2.720 nonbonded pdb=" AO6 COA C1002 " pdb=" AP1 COA C1002 " model vdw 1.868 2.720 ... (remaining 100041 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 9.960 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 34.770 Find NCS groups from input model: 0.860 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.082 2.437 11948 Z= 5.368 Angle : 3.736 77.929 16244 Z= 1.276 Chirality : 0.043 0.401 1804 Planarity : 0.024 0.523 2036 Dihedral : 15.165 170.393 4396 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.41 % Allowed : 4.23 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.80 (0.21), residues: 1516 helix: 2.34 (0.17), residues: 812 sheet: -1.12 (0.36), residues: 184 loop : 0.35 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 190 HIS 0.002 0.001 HIS D 64 PHE 0.008 0.001 PHE C 152 TYR 0.013 0.002 TYR C 382 ARG 0.003 0.000 ARG D 380 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 202 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 0 residues processed: 202 average time/residue: 0.2512 time to fit residues: 72.0045 Evaluate side-chains 105 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 0.2980 chunk 88 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 119 ASN ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN A 292 ASN B 43 GLN B 119 ASN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN B 292 ASN C 43 GLN C 119 ASN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 GLN C 292 ASN D 43 GLN D 119 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN D 292 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 11948 Z= 0.297 Angle : 2.008 56.138 16244 Z= 0.692 Chirality : 0.039 0.263 1804 Planarity : 0.004 0.034 2036 Dihedral : 17.348 178.962 1840 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.14 % Allowed : 7.75 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.52 (0.22), residues: 1516 helix: 3.03 (0.17), residues: 808 sheet: -0.52 (0.34), residues: 216 loop : 0.44 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 185 HIS 0.002 0.001 HIS D 38 PHE 0.031 0.001 PHE C 261 TYR 0.013 0.001 TYR B 391 ARG 0.002 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 143 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 TYR cc_start: 0.7774 (t80) cc_final: 0.7573 (t80) outliers start: 13 outliers final: 4 residues processed: 135 average time/residue: 0.1981 time to fit residues: 41.7741 Evaluate side-chains 119 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain D residue 95 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 11948 Z= 0.280 Angle : 1.977 53.103 16244 Z= 0.679 Chirality : 0.036 0.125 1804 Planarity : 0.004 0.032 2036 Dihedral : 16.022 166.945 1840 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.06 % Allowed : 9.15 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.67 (0.21), residues: 1516 helix: 3.14 (0.17), residues: 808 sheet: -0.47 (0.34), residues: 216 loop : 0.54 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 185 HIS 0.002 0.001 HIS B 64 PHE 0.015 0.001 PHE B 261 TYR 0.014 0.001 TYR B 391 ARG 0.002 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 143 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.327 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 134 average time/residue: 0.2117 time to fit residues: 43.1988 Evaluate side-chains 111 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain D residue 95 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.7925 > 50: distance: 75 - 77: 30.295 distance: 77 - 78: 16.788 distance: 78 - 79: 36.948 distance: 78 - 81: 29.060 distance: 79 - 80: 15.803 distance: 79 - 85: 16.696 distance: 81 - 82: 35.792 distance: 82 - 83: 35.048 distance: 83 - 84: 12.775 distance: 85 - 86: 11.113 distance: 86 - 87: 19.691 distance: 87 - 88: 37.681 distance: 87 - 89: 11.486 distance: 89 - 90: 8.056 distance: 90 - 91: 16.541 distance: 90 - 93: 22.622 distance: 91 - 92: 27.879 distance: 91 - 101: 11.060 distance: 93 - 94: 7.303 distance: 94 - 95: 3.457 distance: 94 - 96: 3.800 distance: 95 - 97: 6.370 distance: 96 - 98: 4.743 distance: 97 - 99: 4.000 distance: 99 - 100: 7.075 distance: 101 - 102: 17.110 distance: 102 - 103: 13.980 distance: 102 - 105: 9.467 distance: 103 - 104: 18.912 distance: 103 - 108: 30.546 distance: 105 - 106: 25.966 distance: 105 - 107: 19.671 distance: 108 - 109: 20.355 distance: 109 - 110: 32.186 distance: 109 - 112: 8.618 distance: 110 - 111: 53.619 distance: 110 - 115: 13.991 distance: 112 - 113: 11.821 distance: 112 - 114: 16.513 distance: 115 - 116: 23.900 distance: 116 - 117: 14.139 distance: 116 - 119: 33.689 distance: 117 - 118: 59.594 distance: 117 - 124: 38.419 distance: 119 - 120: 11.882 distance: 120 - 121: 23.705 distance: 121 - 122: 10.788 distance: 121 - 123: 4.649 distance: 124 - 125: 10.899 distance: 125 - 126: 41.178 distance: 125 - 128: 40.547 distance: 126 - 127: 32.051 distance: 126 - 132: 10.195 distance: 128 - 129: 52.313 distance: 129 - 130: 36.286 distance: 130 - 131: 13.164 distance: 132 - 133: 30.462 distance: 132 - 138: 40.958 distance: 133 - 134: 48.806 distance: 133 - 136: 22.028 distance: 134 - 135: 43.177 distance: 134 - 139: 47.826 distance: 136 - 137: 25.401 distance: 137 - 138: 36.860 distance: 139 - 140: 31.082 distance: 140 - 141: 50.257 distance: 140 - 143: 14.581 distance: 141 - 142: 13.831 distance: 141 - 144: 23.840 distance: 142 - 173: 32.602 distance: 144 - 145: 20.381 distance: 145 - 146: 18.740 distance: 145 - 148: 17.323 distance: 146 - 153: 30.612 distance: 147 - 179: 32.791 distance: 148 - 149: 21.629 distance: 149 - 150: 6.262 distance: 150 - 151: 18.260 distance: 150 - 152: 6.265