Starting phenix.real_space_refine (version: dev) on Wed Mar 15 20:46:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uv9_26809/03_2023/7uv9_26809_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uv9_26809/03_2023/7uv9_26809.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uv9_26809/03_2023/7uv9_26809_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uv9_26809/03_2023/7uv9_26809_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uv9_26809/03_2023/7uv9_26809_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uv9_26809/03_2023/7uv9_26809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uv9_26809/03_2023/7uv9_26809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uv9_26809/03_2023/7uv9_26809_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uv9_26809/03_2023/7uv9_26809_updated.pdb" } resolution = 3.2 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= 0.002 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 "K TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 15342 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 815 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3014 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2972 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 3395 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 409, 3395 Unusual residues: {' FE': 1, 'OH0': 1} Classifications: {'peptide': 407, 'undetermined': 2} Link IDs: {'PTRANS': 19, 'TRANS': 387, None: 2} Not linked: pdbres="PRO K 517 " pdbres="OH0 K 701 " Not linked: pdbres="OH0 K 701 " pdbres=" FE K 702 " Chain breaks: 3 Time building chain proxies: 8.87, per 1000 atoms: 0.58 Number of scatterers: 15342 At special positions: 0 Unit cell: (91, 158.34, 152.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 1 26.01 S 33 16.00 P 292 15.00 O 3435 8.00 N 2815 7.00 C 8766 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: 7.47 Conformation dependent library (CDL) restraints added in 1.6 seconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 3 sheets defined 54.0% alpha, 4.0% beta 142 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 6.41 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.553A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 removed outlier: 4.088A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.674A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 47 through 73 removed outlier: 3.684A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 93 through 96 No H-bonds generated for 'chain 'C' and resid 93 through 96' Processing helix chain 'D' and resid 38 through 48 removed outlier: 3.569A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 84 removed outlier: 3.736A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.514A pdb=" N THR D 122 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER D 123 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.370A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 51 through 76 removed outlier: 3.866A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.810A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 28 through 35 Processing helix chain 'G' and resid 47 through 73 removed outlier: 3.604A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'H' and resid 38 through 48 removed outlier: 3.602A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 84 removed outlier: 3.644A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.513A pdb=" N THR H 122 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 59 through 61 No H-bonds generated for 'chain 'K' and resid 59 through 61' Processing helix chain 'K' and resid 64 through 70 Processing helix chain 'K' and resid 95 through 102 Processing helix chain 'K' and resid 123 through 131 Processing helix chain 'K' and resid 134 through 136 No H-bonds generated for 'chain 'K' and resid 134 through 136' Processing helix chain 'K' and resid 154 through 156 No H-bonds generated for 'chain 'K' and resid 154 through 156' Processing helix chain 'K' and resid 161 through 166 removed outlier: 3.516A pdb=" N PHE K 165 " --> pdb=" O SER K 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE K 166 " --> pdb=" O THR K 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 161 through 166' Processing helix chain 'K' and resid 168 through 172 Processing helix chain 'K' and resid 175 through 180 removed outlier: 3.537A pdb=" N SER K 180 " --> pdb=" O HIS K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 190 No H-bonds generated for 'chain 'K' and resid 188 through 190' Processing helix chain 'K' and resid 215 through 217 No H-bonds generated for 'chain 'K' and resid 215 through 217' Processing helix chain 'K' and resid 238 through 250 Processing helix chain 'K' and resid 258 through 261 No H-bonds generated for 'chain 'K' and resid 258 through 261' Processing helix chain 'K' and resid 305 through 317 Processing helix chain 'K' and resid 322 through 324 No H-bonds generated for 'chain 'K' and resid 322 through 324' Processing helix chain 'K' and resid 329 through 345 Processing helix chain 'K' and resid 352 through 362 Processing helix chain 'K' and resid 455 through 470 Processing helix chain 'K' and resid 473 through 476 No H-bonds generated for 'chain 'K' and resid 473 through 476' Processing helix chain 'K' and resid 485 through 498 Processing sheet with id= A, first strand: chain 'K' and resid 76 through 78 removed outlier: 6.615A pdb=" N LEU K 293 " --> pdb=" O HIS K 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 107 through 112 removed outlier: 3.719A pdb=" N LYS K 117 " --> pdb=" O ASP K 112 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 265 through 270 436 hydrogen bonds defined for protein. 1194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 364 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 7.13 Time building geometry restraints manager: 7.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1794 1.30 - 1.44: 5928 1.44 - 1.58: 7861 1.58 - 1.72: 589 1.72 - 1.86: 57 Bond restraints: 16229 Sorted by residual: bond pdb=" C LYS K 79 " pdb=" O LYS K 79 " ideal model delta sigma weight residual 1.236 1.158 0.078 1.26e-02 6.30e+03 3.86e+01 bond pdb=" CA SER K 161 " pdb=" C SER K 161 " ideal model delta sigma weight residual 1.524 1.456 0.068 1.32e-02 5.74e+03 2.64e+01 bond pdb=" CA LEU K 464 " pdb=" C LEU K 464 " ideal model delta sigma weight residual 1.524 1.588 -0.065 1.27e-02 6.20e+03 2.59e+01 bond pdb=" C ILE K 305 " pdb=" O ILE K 305 " ideal model delta sigma weight residual 1.242 1.199 0.043 8.60e-03 1.35e+04 2.51e+01 bond pdb=" CA TYR K 49 " pdb=" C TYR K 49 " ideal model delta sigma weight residual 1.526 1.480 0.046 9.70e-03 1.06e+04 2.27e+01 ... (remaining 16224 not shown) Histogram of bond angle deviations from ideal: 93.23 - 101.47: 220 101.47 - 109.70: 4756 109.70 - 117.94: 8623 117.94 - 126.18: 8618 126.18 - 134.42: 958 Bond angle restraints: 23175 Sorted by residual: angle pdb=" N THR K 237 " pdb=" CA THR K 237 " pdb=" C THR K 237 " ideal model delta sigma weight residual 110.53 103.44 7.09 1.32e+00 5.74e-01 2.89e+01 angle pdb=" N GLY K 481 " pdb=" CA GLY K 481 " pdb=" C GLY K 481 " ideal model delta sigma weight residual 114.67 120.35 -5.68 1.10e+00 8.26e-01 2.67e+01 angle pdb=" N ASP K 491 " pdb=" CA ASP K 491 " pdb=" C ASP K 491 " ideal model delta sigma weight residual 111.36 116.61 -5.25 1.09e+00 8.42e-01 2.32e+01 angle pdb=" N LEU K 359 " pdb=" CA LEU K 359 " pdb=" C LEU K 359 " ideal model delta sigma weight residual 111.33 117.03 -5.70 1.21e+00 6.83e-01 2.22e+01 angle pdb=" N ILE K 311 " pdb=" CA ILE K 311 " pdb=" C ILE K 311 " ideal model delta sigma weight residual 110.42 114.71 -4.29 9.60e-01 1.09e+00 2.00e+01 ... (remaining 23170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 7265 35.26 - 70.53: 1432 70.53 - 105.79: 26 105.79 - 141.05: 1 141.05 - 176.32: 1 Dihedral angle restraints: 8725 sinusoidal: 5346 harmonic: 3379 Sorted by residual: dihedral pdb=" C1 OH0 K 701 " pdb=" C2 OH0 K 701 " pdb=" C3 OH0 K 701 " pdb=" C4 OH0 K 701 " ideal model delta sinusoidal sigma weight residual 166.34 -61.23 -132.43 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 43.68 176.32 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA THR K 218 " pdb=" C THR K 218 " pdb=" N SER K 219 " pdb=" CA SER K 219 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 8722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2227 0.066 - 0.132: 275 0.132 - 0.199: 77 0.199 - 0.265: 19 0.265 - 0.331: 8 Chirality restraints: 2606 Sorted by residual: chirality pdb=" CA PHE K 215 " pdb=" N PHE K 215 " pdb=" C PHE K 215 " pdb=" CB PHE K 215 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA THR K 209 " pdb=" N THR K 209 " pdb=" C THR K 209 " pdb=" CB THR K 209 " both_signs ideal model delta sigma weight residual False 2.53 2.83 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA TYR K 222 " pdb=" N TYR K 222 " pdb=" C TYR K 222 " pdb=" CB TYR K 222 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 2603 not shown) Planarity restraints: 1927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N OH0 K 701 " 0.034 2.00e-02 2.50e+03 1.18e-01 2.09e+02 pdb=" O OH0 K 701 " -0.164 2.00e-02 2.50e+03 pdb=" C5 OH0 K 701 " -0.156 2.00e-02 2.50e+03 pdb=" C6 OH0 K 701 " 0.045 2.00e-02 2.50e+03 pdb=" C7 OH0 K 701 " 0.112 2.00e-02 2.50e+03 pdb=" O3 OH0 K 701 " 0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 221 " 0.055 2.00e-02 2.50e+03 2.67e-02 1.79e+01 pdb=" CG TRP K 221 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP K 221 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP K 221 " -0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP K 221 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP K 221 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP K 221 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 221 " 0.021 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 221 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP K 221 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 247 " 0.049 2.00e-02 2.50e+03 2.65e-02 1.75e+01 pdb=" CG TRP K 247 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP K 247 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP K 247 " -0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP K 247 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP K 247 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP K 247 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 247 " 0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 247 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP K 247 " 0.018 2.00e-02 2.50e+03 ... (remaining 1924 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 6 2.23 - 2.90: 5076 2.90 - 3.56: 21290 3.56 - 4.23: 39701 4.23 - 4.90: 60716 Nonbonded interactions: 126789 Sorted by model distance: nonbonded pdb=" OE1 GLU K 41 " pdb=" NE2 HIS K 45 " model vdw 1.561 2.520 nonbonded pdb=" O OH0 K 701 " pdb="FE FE K 702 " model vdw 2.037 2.260 nonbonded pdb=" OD1 ASP K 214 " pdb="FE FE K 702 " model vdw 2.159 2.260 nonbonded pdb=" O3 OH0 K 701 " pdb="FE FE K 702 " model vdw 2.203 2.260 nonbonded pdb=" NE2 HIS K 212 " pdb="FE FE K 702 " model vdw 2.208 2.340 ... (remaining 126784 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' and resid 43 through 134) selection = (chain 'E' and resid 43 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 6 Type Number sf(0) Gaussians Fe 1 7.16 5 P 292 5.49 5 S 33 5.16 5 C 8766 2.51 5 N 2815 2.21 5 O 3435 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=0.58 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: 1.520 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: 8.710 Check model and map are aligned: 0.230 Process input model: 48.980 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.150 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 0.095 16229 Z= 0.531 Angle : 0.889 8.246 23175 Z= 0.554 Chirality : 0.055 0.331 2606 Planarity : 0.007 0.118 1927 Dihedral : 26.202 176.319 6547 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.25), residues: 1138 helix: 1.94 (0.21), residues: 645 sheet: 0.84 (0.64), residues: 63 loop : -0.99 (0.28), residues: 430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 168 average time/residue: 0.3664 time to fit residues: 83.8739 Evaluate side-chains 137 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.345 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 24 GLN C 104 GLN F 25 ASN K 176 HIS ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 474 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 16229 Z= 0.258 Angle : 0.595 5.326 23175 Z= 0.355 Chirality : 0.039 0.143 2606 Planarity : 0.005 0.048 1927 Dihedral : 29.750 178.790 4230 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.11 (0.25), residues: 1138 helix: 1.80 (0.21), residues: 645 sheet: 0.98 (0.63), residues: 66 loop : -0.99 (0.28), residues: 427 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 142 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 150 average time/residue: 0.3602 time to fit residues: 74.1307 Evaluate side-chains 130 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 1.430 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1363 time to fit residues: 2.8164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 HIS ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 515 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 16229 Z= 0.314 Angle : 0.630 8.191 23175 Z= 0.370 Chirality : 0.040 0.170 2606 Planarity : 0.005 0.051 1927 Dihedral : 29.907 179.721 4230 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.25), residues: 1138 helix: 1.54 (0.20), residues: 652 sheet: 0.55 (0.67), residues: 66 loop : -1.06 (0.28), residues: 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 138 average time/residue: 0.3922 time to fit residues: 73.6422 Evaluate side-chains 121 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.471 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 84 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 120 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 16229 Z= 0.249 Angle : 0.582 10.290 23175 Z= 0.345 Chirality : 0.038 0.153 2606 Planarity : 0.005 0.050 1927 Dihedral : 29.838 178.801 4230 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.25), residues: 1138 helix: 1.57 (0.21), residues: 651 sheet: 0.32 (0.65), residues: 66 loop : -1.19 (0.28), residues: 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 131 average time/residue: 0.3613 time to fit residues: 65.1988 Evaluate side-chains 130 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 1.336 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1444 time to fit residues: 4.1681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 104 GLN K 171 ASN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 16229 Z= 0.243 Angle : 0.579 9.253 23175 Z= 0.343 Chirality : 0.037 0.146 2606 Planarity : 0.005 0.050 1927 Dihedral : 29.826 178.913 4230 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.25), residues: 1138 helix: 1.59 (0.21), residues: 651 sheet: 0.22 (0.66), residues: 66 loop : -1.21 (0.28), residues: 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 1.425 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 128 average time/residue: 0.3700 time to fit residues: 64.8762 Evaluate side-chains 123 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1340 time to fit residues: 2.2245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.2980 chunk 120 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 104 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 308 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16229 Z= 0.185 Angle : 0.553 8.467 23175 Z= 0.330 Chirality : 0.036 0.133 2606 Planarity : 0.004 0.048 1927 Dihedral : 29.786 178.715 4230 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.25), residues: 1138 helix: 1.79 (0.21), residues: 650 sheet: 0.00 (0.66), residues: 68 loop : -1.01 (0.28), residues: 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 1.453 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 129 average time/residue: 0.3762 time to fit residues: 66.7088 Evaluate side-chains 126 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1273 time to fit residues: 2.3408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 104 GLN K 158 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.047 16229 Z= 0.429 Angle : 0.704 9.795 23175 Z= 0.406 Chirality : 0.044 0.150 2606 Planarity : 0.006 0.048 1927 Dihedral : 30.053 179.439 4230 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.25), residues: 1138 helix: 1.22 (0.20), residues: 651 sheet: -0.34 (0.65), residues: 68 loop : -1.40 (0.28), residues: 419 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 1.381 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 131 average time/residue: 0.3637 time to fit residues: 65.8522 Evaluate side-chains 125 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1403 time to fit residues: 2.3111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.0270 chunk 25 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 105 optimal weight: 0.0070 chunk 121 optimal weight: 9.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 16229 Z= 0.166 Angle : 0.545 7.865 23175 Z= 0.326 Chirality : 0.036 0.134 2606 Planarity : 0.004 0.050 1927 Dihedral : 29.747 178.206 4230 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.25), residues: 1138 helix: 1.82 (0.21), residues: 648 sheet: -0.07 (0.68), residues: 68 loop : -1.07 (0.28), residues: 422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.404 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 123 average time/residue: 0.3778 time to fit residues: 63.4785 Evaluate side-chains 121 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.319 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1330 time to fit residues: 1.8969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 104 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 16229 Z= 0.313 Angle : 0.626 9.293 23175 Z= 0.366 Chirality : 0.040 0.169 2606 Planarity : 0.005 0.048 1927 Dihedral : 29.889 179.335 4230 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.25), residues: 1138 helix: 1.40 (0.21), residues: 660 sheet: -0.10 (0.67), residues: 68 loop : -1.41 (0.28), residues: 410 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.404 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 125 average time/residue: 0.3827 time to fit residues: 65.2540 Evaluate side-chains 120 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1332 time to fit residues: 1.8462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 110 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 16229 Z= 0.246 Angle : 0.594 9.006 23175 Z= 0.351 Chirality : 0.038 0.154 2606 Planarity : 0.005 0.048 1927 Dihedral : 29.870 179.544 4230 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.25), residues: 1138 helix: 1.44 (0.21), residues: 666 sheet: -0.15 (0.67), residues: 68 loop : -1.37 (0.28), residues: 404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.417 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 0.3773 time to fit residues: 62.3069 Evaluate side-chains 120 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.314 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1425 time to fit residues: 1.9099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/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-4893/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-4893/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-4893/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-4893/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/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-4893/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-4893/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: 66.9115 > 50: distance: 64 - 80: 10.935 distance: 68 - 84: 33.534 distance: 72 - 92: 29.092 distance: 75 - 80: 12.519 distance: 76 - 100: 23.596 distance: 80 - 81: 18.442 distance: 81 - 82: 14.354 distance: 82 - 83: 20.889 distance: 82 - 84: 12.349 distance: 83 - 108: 20.391 distance: 84 - 85: 19.282 distance: 85 - 86: 17.716 distance: 85 - 88: 33.662 distance: 86 - 87: 7.045 distance: 86 - 92: 12.621 distance: 87 - 114: 44.643 distance: 88 - 89: 13.136 distance: 88 - 90: 41.402 distance: 89 - 91: 5.301 distance: 92 - 93: 20.356 distance: 93 - 94: 4.222 distance: 93 - 96: 11.291 distance: 94 - 95: 33.160 distance: 94 - 100: 30.094 distance: 95 - 125: 18.450 distance: 96 - 97: 33.476 distance: 97 - 98: 17.908 distance: 98 - 99: 36.056 distance: 100 - 101: 4.412 distance: 101 - 102: 28.958 distance: 101 - 104: 36.930 distance: 102 - 103: 32.031 distance: 102 - 108: 4.554 distance: 103 - 132: 66.912 distance: 104 - 105: 12.514 distance: 105 - 106: 4.959 distance: 105 - 107: 57.369 distance: 108 - 109: 40.476 distance: 109 - 110: 4.535 distance: 109 - 112: 7.777 distance: 110 - 111: 11.456 distance: 111 - 140: 11.568 distance: 112 - 113: 17.758 distance: 114 - 115: 3.562 distance: 115 - 116: 5.502 distance: 115 - 118: 9.186 distance: 116 - 125: 56.432 distance: 117 - 148: 6.881 distance: 118 - 119: 28.415 distance: 119 - 120: 5.653 distance: 119 - 121: 5.427 distance: 120 - 122: 5.048 distance: 122 - 124: 14.671 distance: 125 - 126: 15.917 distance: 126 - 127: 8.261 distance: 126 - 129: 5.554 distance: 127 - 128: 16.116 distance: 127 - 132: 6.355 distance: 128 - 156: 25.591 distance: 129 - 130: 40.341 distance: 129 - 131: 19.795 distance: 132 - 133: 38.698 distance: 133 - 134: 25.746 distance: 133 - 136: 25.221 distance: 134 - 135: 14.704 distance: 134 - 140: 19.898 distance: 135 - 163: 27.265 distance: 136 - 137: 4.543 distance: 137 - 138: 6.907 distance: 137 - 139: 40.478 distance: 140 - 141: 11.121 distance: 141 - 142: 8.186 distance: 141 - 144: 20.954 distance: 142 - 143: 5.894 distance: 142 - 148: 22.881 distance: 143 - 171: 35.156 distance: 144 - 145: 7.895 distance: 145 - 146: 17.973 distance: 145 - 147: 33.374 distance: 148 - 149: 24.338 distance: 149 - 150: 35.726 distance: 149 - 152: 17.201 distance: 150 - 151: 19.466 distance: 150 - 156: 14.516 distance: 151 - 180: 20.565 distance: 152 - 153: 6.583 distance: 152 - 154: 14.046 distance: 153 - 155: 7.075 distance: 159 - 185: 3.008