Starting phenix.real_space_refine on Wed Jan 15 11:33:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u0d_26256/01_2025/7u0d_26256.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0d_26256/01_2025/7u0d_26256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u0d_26256/01_2025/7u0d_26256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0d_26256/01_2025/7u0d_26256.map" model { file = "/net/cci-nas-00/data/ceres_data/7u0d_26256/01_2025/7u0d_26256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0d_26256/01_2025/7u0d_26256.cif" } resolution = 4.8 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= -0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5176 2.51 5 N 1373 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8188 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1574 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "M" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1749 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 218} Chain: "N" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1599 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 200} Chain: "O" Number of atoms: 1611 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 215, 1611 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "P" Number of atoms: 1641 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.03, per 1000 atoms: 0.98 Number of scatterers: 8188 At special positions: 0 Unit cell: (93.195, 130.815, 139.365, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1603 8.00 N 1373 7.00 C 5176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS M 153 " - pdb=" SG CYS M 209 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 138 " - pdb=" SG CYS N 197 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 97 " - pdb=" SG CYS O 100B" distance=2.03 Simple disulfide: pdb=" SG CYS O 140 " - pdb=" SG CYS O 196 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG B 601 " - " ASN B 343 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 882.2 milliseconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 24 sheets defined 9.2% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.084A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.549A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 62 through 65 removed outlier: 3.524A pdb=" N LYS M 65 " --> pdb=" O ASP M 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 62 through 65' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'M' and resid 140 through 144 removed outlier: 3.841A pdb=" N THR M 144 " --> pdb=" O SER M 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 202 No H-bonds generated for 'chain 'M' and resid 200 through 202' Processing helix chain 'N' and resid 30 through 34 Processing helix chain 'N' and resid 81 through 85 Processing helix chain 'N' and resid 125 through 131 Processing helix chain 'N' and resid 185 through 192 removed outlier: 3.762A pdb=" N HIS N 192 " --> pdb=" O GLN N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 216 Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'P' and resid 121 through 126 removed outlier: 3.508A pdb=" N GLN P 124 " --> pdb=" O SER P 121 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU P 125 " --> pdb=" O ASP P 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.992A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.575A pdb=" N GLY M 10 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL M 50 " --> pdb=" O TYR M 59 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR M 59 " --> pdb=" O VAL M 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.575A pdb=" N GLY M 10 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL M 115 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 133 through 137 removed outlier: 6.078A pdb=" N TYR M 189 " --> pdb=" O ASP M 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 133 through 137 removed outlier: 6.078A pdb=" N TYR M 189 " --> pdb=" O ASP M 157 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER M 190 " --> pdb=" O VAL M 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 164 through 167 removed outlier: 4.447A pdb=" N TYR M 207 " --> pdb=" O VAL M 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.472A pdb=" N PHE N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLN N 39 " --> pdb=" O THR N 48 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N THR N 48 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.472A pdb=" N PHE N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 118 through 122 removed outlier: 6.025A pdb=" N TYR N 176 " --> pdb=" O ASP N 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 118 through 122 removed outlier: 6.025A pdb=" N TYR N 176 " --> pdb=" O ASP N 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 157 through 158 Processing sheet with id=AB5, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'O' and resid 10 through 11 removed outlier: 6.819A pdb=" N GLU O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'O' and resid 34 through 39 removed outlier: 5.697A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 93 through 94 Processing sheet with id=AB9, first strand: chain 'O' and resid 120 through 124 removed outlier: 3.812A pdb=" N GLY O 139 " --> pdb=" O LEU O 124 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 151 through 152 removed outlier: 4.350A pdb=" N THR O 151 " --> pdb=" O ASN O 199 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN O 199 " --> pdb=" O THR O 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 10 through 12 removed outlier: 3.967A pdb=" N LEU P 11 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 18 through 24 Processing sheet with id=AC4, first strand: chain 'P' and resid 53 through 54 removed outlier: 4.266A pdb=" N SER P 53 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR P 49 " --> pdb=" O SER P 53 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU P 47 " --> pdb=" O TRP P 35 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 131 through 135 Processing sheet with id=AC6, first strand: chain 'P' and resid 146 through 148 273 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.44: 3713 1.44 - 1.65: 4627 1.65 - 1.87: 46 1.87 - 2.08: 2 2.08 - 2.29: 2 Bond restraints: 8390 Sorted by residual: bond pdb=" CD2 TYR O 145 " pdb=" CE2 TYR O 145 " ideal model delta sigma weight residual 1.382 2.292 -0.910 3.00e-02 1.11e+03 9.20e+02 bond pdb=" CD1 TYR O 145 " pdb=" CE1 TYR O 145 " ideal model delta sigma weight residual 1.382 2.277 -0.895 3.00e-02 1.11e+03 8.91e+02 bond pdb=" CE2 TYR O 145 " pdb=" CZ TYR O 145 " ideal model delta sigma weight residual 1.378 1.940 -0.562 2.40e-02 1.74e+03 5.49e+02 bond pdb=" CE1 TYR O 145 " pdb=" CZ TYR O 145 " ideal model delta sigma weight residual 1.378 1.923 -0.545 2.40e-02 1.74e+03 5.16e+02 bond pdb=" CG TYR O 145 " pdb=" CD1 TYR O 145 " ideal model delta sigma weight residual 1.389 1.854 -0.465 2.10e-02 2.27e+03 4.90e+02 ... (remaining 8385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.78: 11403 5.78 - 11.57: 20 11.57 - 17.35: 1 17.35 - 23.14: 0 23.14 - 28.92: 1 Bond angle restraints: 11425 Sorted by residual: angle pdb=" C TYR O 176 " pdb=" N SER O 177 " pdb=" CA SER O 177 " ideal model delta sigma weight residual 122.99 151.91 -28.92 1.41e+00 5.03e-01 4.21e+02 angle pdb=" CA PRO M 198 " pdb=" N PRO M 198 " pdb=" CD PRO M 198 " ideal model delta sigma weight residual 112.00 98.13 13.87 1.40e+00 5.10e-01 9.81e+01 angle pdb=" CA TYR O 176 " pdb=" C TYR O 176 " pdb=" O TYR O 176 " ideal model delta sigma weight residual 120.70 111.54 9.16 1.08e+00 8.57e-01 7.19e+01 angle pdb=" CA PRO B 521 " pdb=" N PRO B 521 " pdb=" CD PRO B 521 " ideal model delta sigma weight residual 112.00 104.30 7.70 1.40e+00 5.10e-01 3.03e+01 angle pdb=" C SER O 177 " pdb=" CA SER O 177 " pdb=" CB SER O 177 " ideal model delta sigma weight residual 109.71 100.98 8.73 1.83e+00 2.99e-01 2.27e+01 ... (remaining 11420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.95: 4887 31.95 - 63.90: 100 63.90 - 95.85: 8 95.85 - 127.80: 0 127.80 - 159.75: 1 Dihedral angle restraints: 4996 sinusoidal: 1907 harmonic: 3089 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 30.20 62.80 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CA VAL P 110 " pdb=" C VAL P 110 " pdb=" N ALA P 111 " pdb=" CA ALA P 111 " ideal model delta harmonic sigma weight residual 180.00 -150.65 -29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ARG B 403 " pdb=" C ARG B 403 " pdb=" N GLY B 404 " pdb=" CA GLY B 404 " ideal model delta harmonic sigma weight residual -180.00 -151.27 -28.73 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 4993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1090 0.069 - 0.138: 176 0.138 - 0.208: 11 0.208 - 0.277: 0 0.277 - 0.346: 1 Chirality restraints: 1278 Sorted by residual: chirality pdb=" CB ILE P 2 " pdb=" CA ILE P 2 " pdb=" CG1 ILE P 2 " pdb=" CG2 ILE P 2 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA MET M 113 " pdb=" N MET M 113 " pdb=" C MET M 113 " pdb=" CB MET M 113 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PRO M 198 " pdb=" N PRO M 198 " pdb=" C PRO M 198 " pdb=" CB PRO M 198 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1275 not shown) Planarity restraints: 1462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.105 5.00e-02 4.00e+02 1.55e-01 3.83e+01 pdb=" N PRO B 521 " 0.267 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 197 " -0.085 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO M 198 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO M 198 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO M 198 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA P 112 " 0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO P 113 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO P 113 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO P 113 " 0.049 5.00e-02 4.00e+02 ... (remaining 1459 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 158 2.63 - 3.20: 7759 3.20 - 3.77: 12535 3.77 - 4.33: 16763 4.33 - 4.90: 26098 Nonbonded interactions: 63313 Sorted by model distance: nonbonded pdb=" CD2 TYR O 145 " pdb=" N SER O 177 " model vdw 2.065 2.736 nonbonded pdb=" OG SER P 12 " pdb=" NH1 ARG P 107 " model vdw 2.091 3.120 nonbonded pdb=" OH TYR O 145 " pdb=" O VAL O 169 " model vdw 2.142 3.040 nonbonded pdb=" O SER O 32 " pdb=" N VAL O 52 " model vdw 2.146 3.120 nonbonded pdb=" CD1 TYR O 145 " pdb=" N SER O 177 " model vdw 2.149 2.736 ... (remaining 63308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 31.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.430 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 : 0.019 0.910 8390 Z= 1.487 Angle : 0.855 28.922 11425 Z= 0.480 Chirality : 0.049 0.346 1278 Planarity : 0.008 0.155 1461 Dihedral : 13.070 159.746 2990 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.68 % Favored : 90.13 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.45 % 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: -1.37 (0.27), residues: 1054 helix: -2.20 (0.79), residues: 43 sheet: -0.22 (0.27), residues: 388 loop : -1.28 (0.27), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 189 HIS 0.004 0.001 HIS M 35 PHE 0.017 0.002 PHE M 68 TYR 0.041 0.002 TYR O 145 ARG 0.010 0.001 ARG P 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 34 MET cc_start: 0.7860 (mmm) cc_final: 0.7654 (mmt) REVERT: M 157 ASP cc_start: 0.9343 (t70) cc_final: 0.9065 (p0) REVERT: N 142 ASP cc_start: 0.8975 (m-30) cc_final: 0.8681 (m-30) REVERT: P 60 ASP cc_start: 0.8730 (p0) cc_final: 0.8426 (p0) REVERT: P 149 LYS cc_start: 0.9646 (tptt) cc_final: 0.9284 (tptp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.2407 time to fit residues: 22.3722 Evaluate side-chains 42 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 95 optimal weight: 0.2980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN P 160 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.037634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.025170 restraints weight = 124215.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.025997 restraints weight = 78950.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.026471 restraints weight = 54604.732| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 8390 Z= 0.304 Angle : 0.761 16.075 11425 Z= 0.401 Chirality : 0.047 0.242 1278 Planarity : 0.006 0.074 1461 Dihedral : 5.713 31.444 1179 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.68 % Favored : 90.04 % Rotamer: Outliers : 0.11 % Allowed : 8.00 % Favored : 91.89 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.53 (0.27), residues: 1054 helix: -2.15 (0.80), residues: 42 sheet: -0.29 (0.27), residues: 377 loop : -1.42 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP O 154 HIS 0.005 0.001 HIS B 505 PHE 0.023 0.002 PHE O 146 TYR 0.061 0.002 TYR O 145 ARG 0.007 0.001 ARG P 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 109 TYR cc_start: 0.7301 (p90) cc_final: 0.6981 (p90) REVERT: O 90 TYR cc_start: 0.9718 (m-10) cc_final: 0.9494 (m-10) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.2565 time to fit residues: 19.1708 Evaluate side-chains 30 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.5748 > 50: distance: 71 - 113: 3.833 distance: 89 - 117: 26.296 distance: 92 - 114: 27.351 distance: 110 - 114: 27.447 distance: 114 - 115: 16.248 distance: 115 - 116: 7.983 distance: 115 - 118: 39.087 distance: 116 - 117: 53.329 distance: 116 - 123: 24.807 distance: 118 - 119: 44.394 distance: 119 - 120: 7.756 distance: 120 - 121: 37.341 distance: 120 - 122: 28.028 distance: 123 - 124: 29.091 distance: 124 - 125: 24.727 distance: 124 - 127: 12.182 distance: 125 - 126: 31.570 distance: 125 - 132: 13.957 distance: 127 - 128: 33.406 distance: 128 - 129: 33.669 distance: 129 - 130: 31.131 distance: 129 - 131: 31.385 distance: 132 - 133: 41.915 distance: 133 - 134: 16.302 distance: 133 - 136: 56.187 distance: 134 - 135: 21.560 distance: 134 - 144: 17.805 distance: 136 - 137: 44.530 distance: 137 - 138: 20.759 distance: 137 - 139: 25.174 distance: 138 - 140: 29.186 distance: 139 - 141: 43.301 distance: 140 - 142: 38.986 distance: 141 - 142: 20.713 distance: 142 - 143: 22.442 distance: 144 - 145: 68.001 distance: 145 - 146: 43.621 distance: 146 - 147: 33.335 distance: 146 - 148: 34.254 distance: 148 - 149: 41.579 distance: 149 - 150: 48.768 distance: 149 - 152: 19.114 distance: 150 - 151: 3.357 distance: 150 - 156: 40.159 distance: 152 - 153: 38.993 distance: 153 - 154: 18.891 distance: 153 - 155: 35.081 distance: 156 - 157: 6.265 distance: 157 - 158: 50.105 distance: 157 - 160: 22.852 distance: 158 - 159: 13.572 distance: 158 - 162: 29.499 distance: 160 - 161: 40.151 distance: 162 - 163: 26.485 distance: 162 - 168: 46.715 distance: 163 - 164: 14.357 distance: 163 - 166: 40.429 distance: 164 - 165: 39.415 distance: 164 - 169: 15.500 distance: 166 - 167: 24.905 distance: 167 - 168: 28.020 distance: 169 - 170: 15.940 distance: 170 - 171: 9.377 distance: 170 - 173: 13.512 distance: 171 - 172: 24.633 distance: 171 - 183: 40.401 distance: 173 - 174: 33.917 distance: 174 - 175: 18.364 distance: 174 - 176: 26.047 distance: 175 - 177: 12.020 distance: 176 - 178: 44.177 distance: 176 - 179: 28.405 distance: 177 - 178: 39.570 distance: 178 - 180: 16.895 distance: 179 - 181: 22.913 distance: 180 - 182: 19.218 distance: 183 - 184: 29.087 distance: 184 - 185: 31.315 distance: 184 - 187: 23.441 distance: 185 - 186: 14.859 distance: 185 - 190: 42.168 distance: 187 - 188: 59.386 distance: 187 - 189: 52.283 distance: 190 - 191: 10.037 distance: 191 - 192: 18.736 distance: 191 - 194: 24.433 distance: 192 - 193: 50.693 distance: 192 - 201: 22.380 distance: 194 - 195: 27.031 distance: 195 - 196: 12.635 distance: 195 - 197: 25.964 distance: 196 - 198: 24.902 distance: 197 - 199: 14.811 distance: 198 - 200: 9.516 distance: 199 - 200: 23.593