Starting phenix.real_space_refine on Tue Jan 14 11:20:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gzz_34406/01_2025/8gzz_34406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gzz_34406/01_2025/8gzz_34406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gzz_34406/01_2025/8gzz_34406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gzz_34406/01_2025/8gzz_34406.map" model { file = "/net/cci-nas-00/data/ceres_data/8gzz_34406/01_2025/8gzz_34406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gzz_34406/01_2025/8gzz_34406.cif" } resolution = 3.52 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= -0.003 sd= 0.027 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 4186 2.51 5 N 1084 2.21 5 O 1262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6568 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "B" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "D" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "F" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "G" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Time building chain proxies: 0.00, per 1000 atoms: 0.00 Number of scatterers: 6568 At special positions: 0 Unit cell: (87.36, 130.624, 79.04, 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 1262 8.00 N 1084 7.00 C 4186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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 D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 50 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 50 " 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=0, symmetry=0 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 1.3 seconds 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1556 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 17 sheets defined 9.6% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.523A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.914A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.056A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.508A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.868A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'E' and resid 63 through 66 Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.092A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 66 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.981A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.572A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.805A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.575A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.741A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.609A pdb=" N GLU D 13 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.717A pdb=" N THR E 20 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 60 through 61 removed outlier: 3.576A pdb=" N CYS E 50 " --> pdb=" O TYR E 60 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP E 33 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 111 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 60 through 61 removed outlier: 3.576A pdb=" N CYS E 50 " --> pdb=" O TYR E 60 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP E 33 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.668A pdb=" N GLU F 13 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.738A pdb=" N THR G 20 " --> pdb=" O SER G 6 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 60 through 61 removed outlier: 6.646A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET G 34 " --> pdb=" O CYS G 50 " (cutoff:3.500A) 197 hydrogen bonds defined for protein. 459 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: 1.87 Time building geometry restraints manager: 0.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2082 1.34 - 1.47: 1820 1.47 - 1.59: 2798 1.59 - 1.71: 0 1.71 - 1.83: 42 Bond restraints: 6742 Sorted by residual: bond pdb=" C LYS A 356 " pdb=" N ARG A 357 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.32e-02 5.74e+03 1.02e+01 bond pdb=" C GLN F 24 " pdb=" N ALA F 25 " ideal model delta sigma weight residual 1.329 1.285 0.044 1.44e-02 4.82e+03 9.46e+00 bond pdb=" C CYS F 23 " pdb=" N GLN F 24 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.44e-02 4.82e+03 7.41e+00 bond pdb=" N GLN F 24 " pdb=" CA GLN F 24 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.23e-02 6.61e+03 6.89e+00 bond pdb=" N TYR A 449 " pdb=" CA TYR A 449 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.08e-02 8.57e+03 6.79e+00 ... (remaining 6737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 8628 1.15 - 2.31: 435 2.31 - 3.46: 91 3.46 - 4.62: 24 4.62 - 5.77: 6 Bond angle restraints: 9184 Sorted by residual: angle pdb=" C TYR F 49 " pdb=" CA TYR F 49 " pdb=" CB TYR F 49 " ideal model delta sigma weight residual 109.80 115.57 -5.77 1.65e+00 3.67e-01 1.22e+01 angle pdb=" C LYS A 356 " pdb=" N ARG A 357 " pdb=" CA ARG A 357 " ideal model delta sigma weight residual 123.00 118.33 4.67 1.38e+00 5.25e-01 1.15e+01 angle pdb=" CA GLN A 414 " pdb=" C GLN A 414 " pdb=" O GLN A 414 " ideal model delta sigma weight residual 121.56 118.05 3.51 1.09e+00 8.42e-01 1.04e+01 angle pdb=" N TYR F 49 " pdb=" CA TYR F 49 " pdb=" C TYR F 49 " ideal model delta sigma weight residual 110.42 105.78 4.64 1.55e+00 4.16e-01 8.96e+00 angle pdb=" N PHE A 377 " pdb=" CA PHE A 377 " pdb=" C PHE A 377 " ideal model delta sigma weight residual 112.72 109.48 3.24 1.14e+00 7.69e-01 8.09e+00 ... (remaining 9179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3617 17.80 - 35.61: 289 35.61 - 53.41: 29 53.41 - 71.22: 7 71.22 - 89.02: 4 Dihedral angle restraints: 3946 sinusoidal: 1490 harmonic: 2456 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 24.54 68.46 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 26.66 66.34 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" CA CYS A 379 " pdb=" C CYS A 379 " pdb=" N TYR A 380 " pdb=" CA TYR A 380 " ideal model delta harmonic sigma weight residual -180.00 -161.72 -18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 529 0.030 - 0.059: 314 0.059 - 0.089: 88 0.089 - 0.118: 57 0.118 - 0.148: 12 Chirality restraints: 1000 Sorted by residual: chirality pdb=" CA ILE F 21 " pdb=" N ILE F 21 " pdb=" C ILE F 21 " pdb=" CB ILE F 21 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA GLN F 24 " pdb=" N GLN F 24 " pdb=" C GLN F 24 " pdb=" CB GLN F 24 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA GLU B 465 " pdb=" N GLU B 465 " pdb=" C GLU B 465 " pdb=" CB GLU B 465 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 997 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 48 " -0.007 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C ILE F 48 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE F 48 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR F 49 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 24 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.21e+00 pdb=" C GLN F 24 " 0.026 2.00e-02 2.50e+03 pdb=" O GLN F 24 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA F 25 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 49 " -0.012 2.00e-02 2.50e+03 9.52e-03 1.81e+00 pdb=" CG TYR D 49 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR D 49 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR D 49 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 49 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 49 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 49 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 49 " -0.001 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1441 2.78 - 3.31: 5887 3.31 - 3.84: 10276 3.84 - 4.37: 12188 4.37 - 4.90: 21752 Nonbonded interactions: 51544 Sorted by model distance: nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR G 103 " model vdw 2.248 3.040 nonbonded pdb=" O SER E 29 " pdb=" OG1 THR E 53 " model vdw 2.299 3.040 nonbonded pdb=" O SER G 29 " pdb=" OG1 THR G 53 " model vdw 2.334 3.040 nonbonded pdb=" NE2 GLN F 90 " pdb=" O SER F 93 " model vdw 2.337 3.120 nonbonded pdb=" OD2 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.340 3.040 ... (remaining 51539 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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: 28.420 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: 11.600 Find NCS groups from input model: 0.220 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 : 0.004 0.044 6742 Z= 0.281 Angle : 0.620 5.770 9184 Z= 0.361 Chirality : 0.044 0.148 1000 Planarity : 0.003 0.028 1184 Dihedral : 12.188 89.023 2348 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.99 (0.28), residues: 842 helix: -3.59 (0.49), residues: 54 sheet: 0.41 (0.33), residues: 264 loop : -0.90 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.002 0.001 HIS A 505 PHE 0.021 0.002 PHE A 347 TYR 0.023 0.001 TYR D 49 ARG 0.002 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.780 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2289 time to fit residues: 33.5645 Evaluate side-chains 93 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.2980 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 0.0050 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN D 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.084368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.070277 restraints weight = 16509.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.072935 restraints weight = 7962.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.074648 restraints weight = 5085.284| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6742 Z= 0.198 Angle : 0.537 4.999 9184 Z= 0.289 Chirality : 0.043 0.145 1000 Planarity : 0.004 0.040 1184 Dihedral : 4.186 16.306 932 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.85 % Allowed : 7.89 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.05 (0.29), residues: 842 helix: -3.92 (0.42), residues: 54 sheet: 0.24 (0.32), residues: 292 loop : -0.89 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.001 0.000 HIS A 505 PHE 0.045 0.001 PHE B 374 TYR 0.011 0.001 TYR A 380 ARG 0.005 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8592 (m-30) cc_final: 0.8345 (t0) REVERT: D 82 ASP cc_start: 0.7530 (m-30) cc_final: 0.7084 (m-30) REVERT: D 96 ASP cc_start: 0.8085 (p0) cc_final: 0.7181 (p0) outliers start: 6 outliers final: 4 residues processed: 102 average time/residue: 0.1944 time to fit residues: 26.3617 Evaluate side-chains 96 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 18 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 0.0040 chunk 51 optimal weight: 2.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.083384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.069676 restraints weight = 16535.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.072290 restraints weight = 7853.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.073964 restraints weight = 4972.977| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6742 Z= 0.207 Angle : 0.506 4.716 9184 Z= 0.272 Chirality : 0.042 0.140 1000 Planarity : 0.004 0.035 1184 Dihedral : 4.138 15.563 932 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.69 % Allowed : 9.86 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.04 (0.29), residues: 842 helix: -4.02 (0.42), residues: 54 sheet: 0.26 (0.32), residues: 284 loop : -0.85 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.001 0.000 HIS A 505 PHE 0.010 0.001 PHE A 347 TYR 0.011 0.001 TYR A 380 ARG 0.003 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: B 376 THR cc_start: 0.8755 (m) cc_final: 0.8158 (p) REVERT: B 420 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8290 (t0) REVERT: D 96 ASP cc_start: 0.8078 (p0) cc_final: 0.7156 (p0) outliers start: 12 outliers final: 8 residues processed: 103 average time/residue: 0.1835 time to fit residues: 25.5263 Evaluate side-chains 104 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 50.6858 > 50: distance: 16 - 156: 24.058 distance: 17 - 150: 14.551 distance: 20 - 147: 20.381 distance: 72 - 77: 13.221 distance: 77 - 78: 5.510 distance: 78 - 81: 7.556 distance: 79 - 80: 6.441 distance: 79 - 89: 8.081 distance: 81 - 82: 20.229 distance: 82 - 83: 6.768 distance: 82 - 84: 8.270 distance: 83 - 85: 11.155 distance: 84 - 86: 15.494 distance: 85 - 87: 7.563 distance: 86 - 87: 7.074 distance: 87 - 88: 26.562 distance: 89 - 90: 31.548 distance: 90 - 91: 43.506 distance: 90 - 93: 23.751 distance: 91 - 92: 37.961 distance: 91 - 98: 37.985 distance: 93 - 94: 19.771 distance: 94 - 95: 31.362 distance: 95 - 96: 21.571 distance: 96 - 97: 21.120 distance: 98 - 99: 17.410 distance: 99 - 100: 19.947 distance: 99 - 102: 29.905 distance: 100 - 101: 19.522 distance: 100 - 106: 15.862 distance: 102 - 103: 34.745 distance: 103 - 104: 12.869 distance: 103 - 105: 17.535 distance: 106 - 107: 10.910 distance: 106 - 112: 19.521 distance: 107 - 108: 11.859 distance: 107 - 110: 20.088 distance: 108 - 109: 13.854 distance: 108 - 113: 21.370 distance: 110 - 111: 15.563 distance: 111 - 112: 33.777 distance: 113 - 114: 23.274 distance: 114 - 115: 19.210 distance: 114 - 117: 21.433 distance: 115 - 116: 4.730 distance: 115 - 121: 15.452 distance: 117 - 118: 13.147 distance: 118 - 119: 11.478 distance: 118 - 120: 10.526 distance: 121 - 122: 21.725 distance: 122 - 123: 10.106 distance: 122 - 125: 13.578 distance: 123 - 124: 16.372 distance: 123 - 129: 9.586 distance: 125 - 126: 14.738 distance: 126 - 127: 24.202 distance: 126 - 128: 24.938 distance: 129 - 130: 25.635 distance: 130 - 131: 11.167 distance: 130 - 133: 22.502 distance: 131 - 132: 15.479 distance: 131 - 140: 4.804 distance: 133 - 134: 20.923 distance: 134 - 135: 6.687 distance: 134 - 136: 9.169 distance: 135 - 137: 6.939 distance: 136 - 138: 3.366 distance: 137 - 139: 10.822 distance: 140 - 141: 23.063 distance: 141 - 142: 17.600 distance: 141 - 144: 23.568 distance: 142 - 143: 12.295 distance: 142 - 147: 20.592 distance: 144 - 145: 18.653 distance: 144 - 146: 8.718 distance: 147 - 148: 32.170 distance: 148 - 149: 37.666 distance: 149 - 150: 32.103 distance: 149 - 151: 45.180 distance: 151 - 152: 19.155 distance: 151 - 204: 22.465 distance: 152 - 153: 15.043 distance: 152 - 155: 24.693 distance: 153 - 154: 15.892 distance: 153 - 157: 23.271 distance: 154 - 201: 17.831 distance: 155 - 156: 20.914