Starting phenix.real_space_refine on Tue May 7 03:53:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8in8_35592/05_2024/8in8_35592.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8in8_35592/05_2024/8in8_35592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8in8_35592/05_2024/8in8_35592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8in8_35592/05_2024/8in8_35592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8in8_35592/05_2024/8in8_35592.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8in8_35592/05_2024/8in8_35592.pdb" } resolution = 3.0 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= 0.072 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: 6 Type Number sf(0) Gaussians P 47 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 4098 2.51 5 N 1140 2.21 5 O 1355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 455": "OD1" <-> "OD2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "C GLU 330": "OE1" <-> "OE2" Residue "C TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 6663 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2009 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 244} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3685 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 28, 'TRANS': 441} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "I" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 506 Classifications: {'RNA': 24} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 13} Link IDs: {'rna2p': 2, 'rna3p': 21} Chain: "J" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 462 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.51, per 1000 atoms: 0.68 Number of scatterers: 6663 At special positions: 0 Unit cell: (71.6214, 87.0336, 107.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 47 15.00 Mg 1 11.99 O 1355 8.00 N 1140 7.00 C 4098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 36.0% alpha, 20.7% beta 17 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'B' and resid 356 through 367 Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.604A pdb=" N ILE B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 414 Processing helix chain 'B' and resid 414 through 430 removed outlier: 3.694A pdb=" N LYS B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 459 through 466 removed outlier: 3.616A pdb=" N ALA B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 519 removed outlier: 3.688A pdb=" N ARG B 516 " --> pdb=" O PRO B 513 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLU B 518 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 519 " --> pdb=" O ARG B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 529 Processing helix chain 'B' and resid 532 through 549 Processing helix chain 'C' and resid 29 through 37 Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'C' and resid 60 through 73 removed outlier: 3.693A pdb=" N LEU C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 95 Processing helix chain 'C' and resid 111 through 120 removed outlier: 4.191A pdb=" N GLY C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 134 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 151 through 157 removed outlier: 4.931A pdb=" N LYS C 156 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 184 through 190 removed outlier: 3.736A pdb=" N LEU C 188 " --> pdb=" O ASN C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 208 removed outlier: 4.008A pdb=" N VAL C 196 " --> pdb=" O CYS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 295 removed outlier: 3.542A pdb=" N LYS C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 322 Processing helix chain 'C' and resid 418 through 430 removed outlier: 3.872A pdb=" N LYS C 430 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 459 Processing helix chain 'C' and resid 470 through 473 removed outlier: 3.997A pdb=" N MET C 473 " --> pdb=" O ARG C 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 470 through 473' Processing sheet with id=AA1, first strand: chain 'B' and resid 579 through 581 removed outlier: 3.812A pdb=" N ALA C 355 " --> pdb=" O ASP C 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 335 through 337 removed outlier: 4.098A pdb=" N HIS B 444 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AA4, first strand: chain 'B' and resid 371 through 373 removed outlier: 3.819A pdb=" N VAL B 378 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 556 through 561 Processing sheet with id=AA6, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA7, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AA8, first strand: chain 'C' and resid 106 through 108 removed outlier: 3.939A pdb=" N CYS C 107 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C 56 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA C 53 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TYR C 149 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU C 55 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 159 through 160 removed outlier: 3.550A pdb=" N TYR C 160 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 307 removed outlier: 4.151A pdb=" N TYR C 224 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR C 467 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 302 through 303 Processing sheet with id=AB3, first strand: chain 'C' and resid 381 through 382 255 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1657 1.33 - 1.45: 1554 1.45 - 1.57: 3578 1.57 - 1.69: 92 1.69 - 1.81: 32 Bond restraints: 6913 Sorted by residual: bond pdb=" C3' DA J 1 " pdb=" O3' DA J 1 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CB ARG C 138 " pdb=" CG ARG C 138 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" C3' DC J -1 " pdb=" O3' DC J -1 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" CG LEU B 426 " pdb=" CD1 LEU B 426 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" CG PRO C 273 " pdb=" CD PRO C 273 " ideal model delta sigma weight residual 1.503 1.468 0.035 3.40e-02 8.65e+02 1.05e+00 ... (remaining 6908 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.57: 439 106.57 - 113.42: 3746 113.42 - 120.27: 2458 120.27 - 127.13: 2776 127.13 - 133.98: 167 Bond angle restraints: 9586 Sorted by residual: angle pdb=" CA GLU B 508 " pdb=" CB GLU B 508 " pdb=" CG GLU B 508 " ideal model delta sigma weight residual 114.10 121.58 -7.48 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA LEU C 98 " pdb=" CB LEU C 98 " pdb=" CG LEU C 98 " ideal model delta sigma weight residual 116.30 128.89 -12.59 3.50e+00 8.16e-02 1.29e+01 angle pdb=" CB MET C 299 " pdb=" CG MET C 299 " pdb=" SD MET C 299 " ideal model delta sigma weight residual 112.70 121.32 -8.62 3.00e+00 1.11e-01 8.25e+00 angle pdb=" CA ARG C 138 " pdb=" CB ARG C 138 " pdb=" CG ARG C 138 " ideal model delta sigma weight residual 114.10 119.46 -5.36 2.00e+00 2.50e-01 7.17e+00 angle pdb=" CA PRO C 273 " pdb=" N PRO C 273 " pdb=" CD PRO C 273 " ideal model delta sigma weight residual 112.00 108.37 3.63 1.40e+00 5.10e-01 6.73e+00 ... (remaining 9581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 3813 35.12 - 70.25: 289 70.25 - 105.37: 15 105.37 - 140.50: 1 140.50 - 175.62: 3 Dihedral angle restraints: 4121 sinusoidal: 2018 harmonic: 2103 Sorted by residual: dihedral pdb=" CA PHE B 328 " pdb=" C PHE B 328 " pdb=" N PRO B 329 " pdb=" CA PRO B 329 " ideal model delta harmonic sigma weight residual 180.00 153.35 26.65 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA VAL C 463 " pdb=" C VAL C 463 " pdb=" N ASN C 464 " pdb=" CA ASN C 464 " ideal model delta harmonic sigma weight residual -180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA ILE C 14 " pdb=" C ILE C 14 " pdb=" N PRO C 15 " pdb=" CA PRO C 15 " ideal model delta harmonic sigma weight residual 180.00 -157.56 -22.44 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 4118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 684 0.029 - 0.059: 269 0.059 - 0.088: 71 0.088 - 0.117: 45 0.117 - 0.147: 17 Chirality restraints: 1086 Sorted by residual: chirality pdb=" C1' G I 7 " pdb=" O4' G I 7 " pdb=" C2' G I 7 " pdb=" N9 G I 7 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE C 407 " pdb=" N ILE C 407 " pdb=" C ILE C 407 " pdb=" CB ILE C 407 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CB ILE C 305 " pdb=" CA ILE C 305 " pdb=" CG1 ILE C 305 " pdb=" CG2 ILE C 305 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 1083 not shown) Planarity restraints: 1063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 272 " 0.058 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO C 273 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 273 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 273 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 56 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO C 57 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 57 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 57 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U I 5 " 0.025 2.00e-02 2.50e+03 1.25e-02 3.53e+00 pdb=" N1 U I 5 " -0.026 2.00e-02 2.50e+03 pdb=" C2 U I 5 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U I 5 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U I 5 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U I 5 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U I 5 " 0.007 2.00e-02 2.50e+03 pdb=" C5 U I 5 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U I 5 " -0.005 2.00e-02 2.50e+03 ... (remaining 1060 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 43 2.54 - 3.13: 4720 3.13 - 3.72: 10334 3.72 - 4.31: 14501 4.31 - 4.90: 23667 Nonbonded interactions: 53265 Sorted by model distance: nonbonded pdb=" OP1 A I 1 " pdb="MG MG I 101 " model vdw 1.950 2.170 nonbonded pdb=" OP3 A I 1 " pdb="MG MG I 101 " model vdw 2.001 2.170 nonbonded pdb=" O MET C 473 " pdb="MG MG I 101 " model vdw 2.015 2.170 nonbonded pdb=" O GLN C 281 " pdb=" OG SER C 285 " model vdw 2.225 2.440 nonbonded pdb=" O LEU C 426 " pdb=" OG1 THR C 429 " model vdw 2.233 2.440 ... (remaining 53260 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: 1.080 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: 3.380 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.730 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 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 : 0.003 0.046 6913 Z= 0.187 Angle : 0.615 12.588 9586 Z= 0.325 Chirality : 0.040 0.147 1086 Planarity : 0.005 0.086 1063 Dihedral : 21.500 175.621 2769 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.13 % Favored : 93.73 % Rotamer: Outliers : 3.63 % Allowed : 33.50 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.30 (0.32), residues: 718 helix: 1.49 (0.37), residues: 211 sheet: -0.16 (0.44), residues: 160 loop : -1.30 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.003 0.001 HIS B 437 PHE 0.010 0.001 PHE C 158 TYR 0.013 0.001 TYR C 469 ARG 0.008 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 56 time to evaluate : 0.658 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 21 residues processed: 75 average time/residue: 0.9377 time to fit residues: 75.3969 Evaluate side-chains 74 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 53 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 447 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 0.0980 chunk 23 optimal weight: 0.0980 chunk 36 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6913 Z= 0.185 Angle : 0.556 8.192 9586 Z= 0.294 Chirality : 0.040 0.145 1086 Planarity : 0.005 0.055 1063 Dihedral : 19.517 173.718 1455 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.95 % Allowed : 31.85 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.15 (0.32), residues: 718 helix: 1.61 (0.36), residues: 224 sheet: 0.04 (0.44), residues: 156 loop : -1.38 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 377 HIS 0.003 0.001 HIS C 166 PHE 0.008 0.001 PHE C 248 TYR 0.012 0.001 TYR C 341 ARG 0.006 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 61 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: C 436 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.7071 (p0) outliers start: 30 outliers final: 13 residues processed: 86 average time/residue: 0.9234 time to fit residues: 85.1335 Evaluate side-chains 73 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 462 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6913 Z= 0.311 Angle : 0.642 7.634 9586 Z= 0.339 Chirality : 0.045 0.208 1086 Planarity : 0.005 0.056 1063 Dihedral : 19.616 175.759 1439 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.55 % Favored : 93.31 % Rotamer: Outliers : 6.60 % Allowed : 32.01 % Favored : 61.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.50 (0.32), residues: 718 helix: 1.35 (0.37), residues: 222 sheet: -0.05 (0.44), residues: 150 loop : -1.64 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 377 HIS 0.004 0.001 HIS B 444 PHE 0.012 0.002 PHE C 143 TYR 0.026 0.002 TYR C 341 ARG 0.006 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 62 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: B 418 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6398 (tptp) REVERT: B 528 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7144 (ttt-90) REVERT: C 130 VAL cc_start: 0.7429 (OUTLIER) cc_final: 0.7141 (p) REVERT: C 260 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.7004 (p90) REVERT: C 436 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.7148 (p0) outliers start: 40 outliers final: 15 residues processed: 92 average time/residue: 1.0606 time to fit residues: 103.7099 Evaluate side-chains 80 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 436 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6913 Z= 0.269 Angle : 0.614 7.608 9586 Z= 0.326 Chirality : 0.043 0.181 1086 Planarity : 0.005 0.055 1063 Dihedral : 19.621 174.427 1438 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.27 % Favored : 93.59 % Rotamer: Outliers : 6.11 % Allowed : 32.18 % Favored : 61.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.45 (0.32), residues: 718 helix: 1.42 (0.37), residues: 217 sheet: -0.06 (0.44), residues: 150 loop : -1.56 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 377 HIS 0.003 0.001 HIS B 444 PHE 0.010 0.001 PHE C 143 TYR 0.021 0.002 TYR C 341 ARG 0.006 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 62 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: B 528 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6876 (ttm170) REVERT: C 260 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7414 (p90) REVERT: C 352 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.5996 (tttt) REVERT: C 436 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7123 (p0) outliers start: 37 outliers final: 14 residues processed: 88 average time/residue: 1.0375 time to fit residues: 97.1195 Evaluate side-chains 75 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 436 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/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-5322/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-5322/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-5322/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-5322/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-5322/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-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/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-5322/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-5322/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: 72.8639 > 50: distance: 36 - 61: 34.607 distance: 40 - 67: 33.010 distance: 44 - 73: 33.461 distance: 55 - 61: 34.724 distance: 61 - 62: 56.311 distance: 62 - 63: 39.140 distance: 62 - 65: 56.366 distance: 63 - 64: 57.316 distance: 63 - 67: 40.525 distance: 65 - 66: 40.215 distance: 67 - 68: 39.944 distance: 68 - 69: 57.135 distance: 68 - 71: 58.043 distance: 69 - 70: 56.544 distance: 69 - 73: 56.889 distance: 71 - 72: 57.387 distance: 73 - 74: 69.168 distance: 74 - 75: 39.570 distance: 75 - 76: 57.731 distance: 75 - 83: 57.515 distance: 77 - 78: 38.695 distance: 78 - 79: 40.319 distance: 78 - 80: 38.740 distance: 80 - 82: 39.983 distance: 81 - 82: 40.056 distance: 83 - 84: 25.984 distance: 84 - 85: 26.886 distance: 84 - 87: 61.411 distance: 85 - 86: 56.586 distance: 85 - 91: 56.880 distance: 87 - 88: 41.160 distance: 88 - 89: 55.810 distance: 88 - 90: 57.314 distance: 91 - 92: 41.035 distance: 92 - 93: 57.574 distance: 93 - 94: 40.651 distance: 93 - 95: 39.992 distance: 95 - 96: 69.623 distance: 96 - 99: 57.861 distance: 97 - 98: 56.360 distance: 99 - 100: 40.022 distance: 100 - 101: 39.863 distance: 101 - 102: 69.678 distance: 102 - 103: 40.746 distance: 106 - 107: 55.588 distance: 107 - 108: 57.671 distance: 107 - 110: 39.007 distance: 108 - 109: 39.788 distance: 108 - 114: 55.869 distance: 110 - 111: 57.380 distance: 112 - 113: 56.150 distance: 114 - 120: 56.539 distance: 115 - 116: 55.079 distance: 116 - 117: 70.382 distance: 116 - 121: 56.908 distance: 118 - 119: 44.819 distance: 119 - 120: 22.497 distance: 121 - 122: 55.497 distance: 122 - 123: 56.660 distance: 123 - 124: 55.372 distance: 123 - 132: 41.723 distance: 126 - 127: 10.547 distance: 127 - 128: 64.951 distance: 129 - 130: 42.627 distance: 129 - 131: 68.744 distance: 132 - 133: 48.151 distance: 133 - 136: 40.030 distance: 134 - 135: 68.172 distance: 134 - 141: 34.941 distance: 136 - 137: 57.041 distance: 137 - 138: 40.137 distance: 139 - 140: 55.625