Starting phenix.real_space_refine on Sun Mar 10 23:24:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/03_2024/7m3n_23658.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/03_2024/7m3n_23658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/03_2024/7m3n_23658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/03_2024/7m3n_23658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/03_2024/7m3n_23658.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/03_2024/7m3n_23658.pdb" } resolution = 2.4 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.047 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 23 5.16 5 C 3813 2.51 5 N 1024 2.21 5 O 1144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ASP 1": "OD1" <-> "OD2" Residue "L ASP 17": "OD1" <-> "OD2" Residue "L ASP 28": "OD1" <-> "OD2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A ASP 373": "OD1" <-> "OD2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A ASP 475": "OD1" <-> "OD2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A ASP 511": "OD1" <-> "OD2" Residue "A ASP 526": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6004 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 842 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 103} Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 924 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "A" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Time building chain proxies: 3.67, per 1000 atoms: 0.61 Number of scatterers: 6004 At special positions: 0 Unit cell: (82.5, 113.3, 105.6, 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 23 16.00 O 1144 8.00 N 1024 7.00 C 3813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 494 " distance=2.04 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: 2.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 17 sheets defined 9.6% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.611A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.533A pdb=" N VAL A 119 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.979A pdb=" N MET A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.853A pdb=" N VAL A 241 " --> pdb=" O PRO A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.037A pdb=" N LEU A 285 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 removed outlier: 4.099A pdb=" N ARG A 313 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.192A pdb=" N GLY A 385 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 removed outlier: 3.556A pdb=" N ASP A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.722A pdb=" N PHE A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.692A pdb=" N ASN A 560 " --> pdb=" O ASN A 557 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 561 " --> pdb=" O GLN A 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 557 through 561' Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.687A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.685A pdb=" N VAL L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.526A pdb=" N SER L 65 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.443A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.979A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 60 removed outlier: 6.655A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 60 removed outlier: 6.655A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 49 through 53 removed outlier: 6.761A pdb=" N TYR A 524 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL A 149 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP A 526 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN A 147 " --> pdb=" O ASP A 526 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP A 528 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A 145 " --> pdb=" O TRP A 528 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS A 530 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN A 143 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS A 532 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE A 141 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A 534 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 538 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A 135 " --> pdb=" O LYS A 538 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLN A 143 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLY A 264 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE A 145 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ALA A 262 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 164 through 167 Processing sheet with id=AA9, first strand: chain 'A' and resid 80 through 84 removed outlier: 4.235A pdb=" N ALA A 103 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TRP A 208 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TRP A 109 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR A 206 " --> pdb=" O TRP A 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 80 through 84 removed outlier: 5.963A pdb=" N VAL A 502 " --> pdb=" O PRO A 108 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 497 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 215 through 218 removed outlier: 6.336A pdb=" N ASP A 215 " --> pdb=" O HIS A 234 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 276 through 278 Processing sheet with id=AB4, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.357A pdb=" N GLU A 335 " --> pdb=" O ALA A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 345 through 348 Processing sheet with id=AB6, first strand: chain 'A' and resid 377 through 380 Processing sheet with id=AB7, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AB8, first strand: chain 'A' and resid 470 through 472 removed outlier: 6.555A pdb=" N ASP A 471 " --> pdb=" O CYS A 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 167 hydrogen bonds defined for protein. 387 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: 1.74 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1949 1.34 - 1.46: 1564 1.46 - 1.58: 2622 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 6173 Sorted by residual: bond pdb=" CA ILE A 219 " pdb=" CB ILE A 219 " ideal model delta sigma weight residual 1.537 1.522 0.015 1.29e-02 6.01e+03 1.36e+00 bond pdb=" CG1 ILE A 101 " pdb=" CD1 ILE A 101 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.09e+00 bond pdb=" CA ASP A 269 " pdb=" C ASP A 269 " ideal model delta sigma weight residual 1.530 1.519 0.011 1.08e-02 8.57e+03 1.04e+00 bond pdb=" CB THR A 230 " pdb=" CG2 THR A 230 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.49e-01 bond pdb=" CB GLN A 143 " pdb=" CG GLN A 143 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 7.83e-01 ... (remaining 6168 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.56: 222 106.56 - 113.43: 3265 113.43 - 120.31: 2160 120.31 - 127.18: 2674 127.18 - 134.06: 99 Bond angle restraints: 8420 Sorted by residual: angle pdb=" C GLY H 54 " pdb=" N ASP H 55 " pdb=" CA ASP H 55 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.48e+00 angle pdb=" N ALA L 32 " pdb=" CA ALA L 32 " pdb=" C ALA L 32 " ideal model delta sigma weight residual 111.30 114.69 -3.39 1.36e+00 5.41e-01 6.21e+00 angle pdb=" N PRO A 423 " pdb=" CA PRO A 423 " pdb=" C PRO A 423 " ideal model delta sigma weight residual 112.47 107.54 4.93 2.06e+00 2.36e-01 5.73e+00 angle pdb=" C LYS H 74 " pdb=" N SER H 75 " pdb=" CA SER H 75 " ideal model delta sigma weight residual 121.54 125.91 -4.37 1.91e+00 2.74e-01 5.23e+00 angle pdb=" CA ASN H 83 " pdb=" C ASN H 83 " pdb=" N ARG H 84 " ideal model delta sigma weight residual 114.17 117.47 -3.30 1.45e+00 4.76e-01 5.18e+00 ... (remaining 8415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 3131 16.94 - 33.88: 353 33.88 - 50.82: 86 50.82 - 67.76: 30 67.76 - 84.70: 6 Dihedral angle restraints: 3606 sinusoidal: 1417 harmonic: 2189 Sorted by residual: dihedral pdb=" CB CYS A 490 " pdb=" SG CYS A 490 " pdb=" SG CYS A 494 " pdb=" CB CYS A 494 " ideal model delta sinusoidal sigma weight residual 93.00 37.65 55.35 1 1.00e+01 1.00e-02 4.14e+01 dihedral pdb=" CA THR L 31 " pdb=" C THR L 31 " pdb=" N ALA L 32 " pdb=" CA ALA L 32 " ideal model delta harmonic sigma weight residual 180.00 151.43 28.57 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASN A 421 " pdb=" C ASN A 421 " pdb=" N LEU A 422 " pdb=" CA LEU A 422 " ideal model delta harmonic sigma weight residual -180.00 -156.12 -23.88 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 3603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 483 0.028 - 0.057: 256 0.057 - 0.085: 99 0.085 - 0.113: 52 0.113 - 0.141: 17 Chirality restraints: 907 Sorted by residual: chirality pdb=" CA ILE L 39 " pdb=" N ILE L 39 " pdb=" C ILE L 39 " pdb=" CB ILE L 39 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 357 " pdb=" N ILE A 357 " pdb=" C ILE A 357 " pdb=" CB ILE A 357 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE A 306 " pdb=" N ILE A 306 " pdb=" C ILE A 306 " pdb=" CB ILE A 306 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 904 not shown) Planarity restraints: 1096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 122 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO A 123 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 464 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO A 465 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 465 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 465 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 55 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C ASP H 55 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP H 55 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY H 56 " 0.010 2.00e-02 2.50e+03 ... (remaining 1093 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 259 2.71 - 3.26: 5360 3.26 - 3.81: 9281 3.81 - 4.35: 11759 4.35 - 4.90: 20009 Nonbonded interactions: 46668 Sorted by model distance: nonbonded pdb=" OG SER L 43 " pdb=" O GLY H 110 " model vdw 2.168 2.440 nonbonded pdb=" NH2 ARG A 382 " pdb=" O GLY A 392 " model vdw 2.220 2.520 nonbonded pdb=" OG SER A 65 " pdb=" O VAL A 119 " model vdw 2.287 2.440 nonbonded pdb=" O THR A 301 " pdb=" OG1 THR A 301 " model vdw 2.324 2.440 nonbonded pdb=" ND2 ASN A 443 " pdb=" OG1 THR A 445 " model vdw 2.346 2.520 ... (remaining 46663 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 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: 6.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 18.890 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.500 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6173 Z= 0.303 Angle : 0.630 8.042 8420 Z= 0.358 Chirality : 0.044 0.141 907 Planarity : 0.005 0.060 1096 Dihedral : 15.949 84.702 2197 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.27 % Favored : 95.59 % Rotamer: Outliers : 4.28 % Allowed : 22.48 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.26), residues: 749 helix: -2.08 (1.08), residues: 10 sheet: -1.02 (0.30), residues: 248 loop : -2.14 (0.22), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.007 0.001 HIS L 91 PHE 0.015 0.002 PHE A 535 TYR 0.019 0.002 TYR A 342 ARG 0.012 0.001 ARG H 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 0.660 Fit side-chains REVERT: L 72 THR cc_start: 0.8624 (m) cc_final: 0.8411 (t) REVERT: L 86 TYR cc_start: 0.8534 (m-80) cc_final: 0.8178 (m-80) REVERT: L 89 GLN cc_start: 0.8053 (tt0) cc_final: 0.7769 (tt0) REVERT: L 97 THR cc_start: 0.8446 (m) cc_final: 0.8226 (p) REVERT: H 5 GLN cc_start: 0.8254 (tp-100) cc_final: 0.7975 (tp40) REVERT: H 8 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.5830 (pp20) REVERT: A 53 PHE cc_start: 0.8535 (m-80) cc_final: 0.8193 (m-80) REVERT: A 125 ASP cc_start: 0.6873 (m-30) cc_final: 0.6624 (m-30) REVERT: A 154 SER cc_start: 0.8050 (t) cc_final: 0.7696 (p) REVERT: A 305 ASP cc_start: 0.8063 (m-30) cc_final: 0.7189 (m-30) REVERT: A 314 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7055 (tpt-90) REVERT: A 319 MET cc_start: 0.7868 (mtp) cc_final: 0.7587 (mtp) REVERT: A 346 GLU cc_start: 0.5765 (tt0) cc_final: 0.4426 (tt0) REVERT: A 475 ASP cc_start: 0.7852 (t0) cc_final: 0.7631 (t0) outliers start: 28 outliers final: 13 residues processed: 175 average time/residue: 0.9501 time to fit residues: 175.6952 Evaluate side-chains 165 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 526 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.0980 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN L 42 GLN L 53 ASN H 5 GLN H 39 GLN H 43 GLN H 81 GLN A 72 ASN A 93 ASN A 104 GLN A 137 HIS A 143 GLN A 222 HIS A 242 GLN A 280 GLN A 296 GLN A 302 ASN A 309 GLN A 384 HIS A 404 GLN A 417 ASN A 428 ASN A 443 ASN A 446 ASN A 458 ASN A 459 ASN A 468 GLN A 560 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6173 Z= 0.181 Angle : 0.517 8.087 8420 Z= 0.266 Chirality : 0.043 0.146 907 Planarity : 0.004 0.064 1096 Dihedral : 6.793 59.071 849 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.74 % Favored : 96.13 % Rotamer: Outliers : 3.67 % Allowed : 24.92 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.70 (0.27), residues: 749 helix: -1.77 (0.89), residues: 16 sheet: -0.36 (0.31), residues: 243 loop : -1.58 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 50 HIS 0.004 0.001 HIS L 91 PHE 0.009 0.001 PHE A 535 TYR 0.011 0.001 TYR A 342 ARG 0.005 0.000 ARG H 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 0.675 Fit side-chains REVERT: L 72 THR cc_start: 0.8622 (m) cc_final: 0.8409 (t) REVERT: H 5 GLN cc_start: 0.8263 (tp40) cc_final: 0.7958 (tp40) REVERT: A 53 PHE cc_start: 0.8516 (m-80) cc_final: 0.8170 (m-80) REVERT: A 125 ASP cc_start: 0.6865 (m-30) cc_final: 0.6554 (m-30) REVERT: A 149 VAL cc_start: 0.8515 (t) cc_final: 0.8294 (p) REVERT: A 154 SER cc_start: 0.8060 (t) cc_final: 0.7764 (p) REVERT: A 298 GLU cc_start: 0.4113 (OUTLIER) cc_final: 0.3115 (mp0) REVERT: A 305 ASP cc_start: 0.8065 (m-30) cc_final: 0.6391 (m-30) REVERT: A 314 ARG cc_start: 0.7629 (mtm180) cc_final: 0.7068 (tpt-90) REVERT: A 475 ASP cc_start: 0.7833 (t0) cc_final: 0.7594 (t0) outliers start: 24 outliers final: 10 residues processed: 170 average time/residue: 0.9123 time to fit residues: 164.3390 Evaluate side-chains 161 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 555 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 63.8854 > 50: distance: 25 - 31: 17.479 distance: 31 - 32: 35.496 distance: 31 - 37: 10.743 distance: 32 - 33: 53.325 distance: 32 - 35: 36.666 distance: 33 - 34: 49.059 distance: 33 - 38: 28.042 distance: 35 - 36: 16.732 distance: 36 - 37: 16.439 distance: 38 - 39: 23.799 distance: 39 - 40: 10.092 distance: 39 - 42: 29.204 distance: 40 - 41: 33.305 distance: 40 - 45: 8.949 distance: 42 - 43: 17.661 distance: 42 - 44: 29.879 distance: 45 - 46: 6.538 distance: 46 - 47: 28.998 distance: 46 - 49: 19.899 distance: 47 - 48: 23.750 distance: 47 - 53: 11.836 distance: 49 - 50: 19.644 distance: 50 - 51: 26.226 distance: 50 - 52: 38.258 distance: 53 - 54: 4.284 distance: 53 - 59: 24.112 distance: 54 - 55: 43.433 distance: 54 - 57: 17.576 distance: 55 - 60: 54.322 distance: 57 - 58: 26.410 distance: 58 - 59: 13.465 distance: 60 - 61: 15.921 distance: 61 - 62: 23.754 distance: 61 - 64: 24.510 distance: 62 - 63: 27.835 distance: 62 - 68: 13.287 distance: 64 - 65: 13.295 distance: 64 - 66: 7.367 distance: 65 - 67: 41.334 distance: 68 - 69: 10.560 distance: 69 - 70: 39.256 distance: 70 - 71: 33.453 distance: 70 - 72: 34.299 distance: 72 - 73: 33.665 distance: 73 - 74: 25.691 distance: 74 - 75: 25.009 distance: 74 - 76: 22.298 distance: 76 - 77: 18.177 distance: 77 - 78: 29.081 distance: 77 - 80: 36.490 distance: 78 - 79: 16.455 distance: 78 - 85: 20.123 distance: 80 - 81: 21.404 distance: 81 - 82: 48.415 distance: 82 - 83: 26.263 distance: 83 - 84: 31.295 distance: 85 - 86: 15.808 distance: 86 - 87: 5.438 distance: 86 - 89: 6.496 distance: 87 - 88: 6.614 distance: 87 - 92: 8.273 distance: 89 - 90: 4.809 distance: 89 - 91: 3.981 distance: 92 - 93: 7.611 distance: 93 - 94: 20.873 distance: 94 - 95: 21.091 distance: 94 - 96: 25.731