Starting phenix.real_space_refine on Sun Mar 10 23:48:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nqk_12528/03_2024/7nqk_12528.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nqk_12528/03_2024/7nqk_12528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nqk_12528/03_2024/7nqk_12528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nqk_12528/03_2024/7nqk_12528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nqk_12528/03_2024/7nqk_12528.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nqk_12528/03_2024/7nqk_12528.pdb" } resolution = 3.5 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= 0.002 sd= 0.044 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 37 5.16 5 C 3998 2.51 5 N 1014 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A ASP 282": "OD1" <-> "OD2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A ASP 532": "OD1" <-> "OD2" Residue "A TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A ASP 576": "OD1" <-> "OD2" Residue "A PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 115": "OE1" <-> "OE2" 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: 6139 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5173 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 24, 'TRANS': 633} Chain: "B" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 966 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Time building chain proxies: 3.79, per 1000 atoms: 0.62 Number of scatterers: 6139 At special positions: 0 Unit cell: (103.168, 113.984, 93.184, 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 37 16.00 O 1090 8.00 N 1014 7.00 C 3998 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 216 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 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: 2.27 Conformation dependent library (CDL) restraints added in 1.3 seconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1456 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 46.1% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 46 through 74 removed outlier: 3.625A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASN A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 59 " --> pdb=" O CYS A 55 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 67 " --> pdb=" O MET A 63 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 96 Processing helix chain 'A' and resid 96 through 106 removed outlier: 4.042A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 130 removed outlier: 3.572A pdb=" N TYR A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 171 removed outlier: 3.533A pdb=" N SER A 146 " --> pdb=" O HIS A 142 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Proline residue: A 162 - end of helix removed outlier: 3.757A pdb=" N ALA A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 202 removed outlier: 4.032A pdb=" N ARG A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 217 through 237 Proline residue: A 224 - end of helix removed outlier: 3.548A pdb=" N VAL A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.635A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.763A pdb=" N PHE A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 346 through 362 removed outlier: 3.608A pdb=" N PHE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Proline residue: A 357 - end of helix Processing helix chain 'A' and resid 362 through 368 Processing helix chain 'A' and resid 377 through 402 Processing helix chain 'A' and resid 611 through 636 removed outlier: 3.612A pdb=" N VAL A 627 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.132A pdb=" N LYS A 642 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 665 removed outlier: 4.141A pdb=" N GLN A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 695 removed outlier: 3.685A pdb=" N TYR A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 53 through 56 removed outlier: 3.801A pdb=" N ARG B 56 " --> pdb=" O TRP B 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'A' and resid 453 through 455 removed outlier: 3.538A pdb=" N LEU A 416 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 414 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N PHE A 415 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU A 489 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN A 417 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE A 491 " --> pdb=" O GLN A 417 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU A 419 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N GLN A 493 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS A 486 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 443 Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 443 removed outlier: 3.832A pdb=" N LEU A 464 " --> pdb=" O HIS A 479 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS A 479 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 544 through 545 removed outlier: 3.588A pdb=" N ASN A 521 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 544 through 545 removed outlier: 3.588A pdb=" N ASN A 521 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 554 through 556 Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AA8, first strand: chain 'B' and resid 20 through 23 Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 60 removed outlier: 5.360A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 891 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: 1.85 Time building geometry restraints manager: 2.50 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: 1908 1.34 - 1.46: 1510 1.46 - 1.58: 2816 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6292 Sorted by residual: bond pdb=" N GLY B 10 " pdb=" CA GLY B 10 " ideal model delta sigma weight residual 1.443 1.485 -0.043 1.17e-02 7.31e+03 1.32e+01 bond pdb=" CA SER B 7 " pdb=" CB SER B 7 " ideal model delta sigma weight residual 1.535 1.485 0.049 1.58e-02 4.01e+03 9.80e+00 bond pdb=" N LEU B 11 " pdb=" CA LEU B 11 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.32e-02 5.74e+03 8.91e+00 bond pdb=" N GLY B 9 " pdb=" CA GLY B 9 " ideal model delta sigma weight residual 1.449 1.486 -0.037 1.24e-02 6.50e+03 8.77e+00 bond pdb=" N GLU B 6 " pdb=" CA GLU B 6 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.62e+00 ... (remaining 6287 not shown) Histogram of bond angle deviations from ideal: 98.16 - 105.33: 103 105.33 - 112.50: 3262 112.50 - 119.67: 2022 119.67 - 126.84: 3067 126.84 - 134.01: 91 Bond angle restraints: 8545 Sorted by residual: angle pdb=" CA GLY B 9 " pdb=" C GLY B 9 " pdb=" N GLY B 10 " ideal model delta sigma weight residual 114.48 120.99 -6.51 1.19e+00 7.06e-01 3.00e+01 angle pdb=" CA GLY B 9 " pdb=" C GLY B 9 " pdb=" O GLY B 9 " ideal model delta sigma weight residual 121.87 116.39 5.48 1.02e+00 9.61e-01 2.88e+01 angle pdb=" CA THR B 124 " pdb=" C THR B 124 " pdb=" O THR B 124 " ideal model delta sigma weight residual 121.60 115.98 5.62 1.21e+00 6.83e-01 2.15e+01 angle pdb=" CA CYS A 211 " pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " ideal model delta sigma weight residual 114.40 124.86 -10.46 2.30e+00 1.89e-01 2.07e+01 angle pdb=" CA VAL B 5 " pdb=" C VAL B 5 " pdb=" O VAL B 5 " ideal model delta sigma weight residual 122.13 117.66 4.47 1.11e+00 8.12e-01 1.62e+01 ... (remaining 8540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 3275 17.45 - 34.90: 338 34.90 - 52.35: 58 52.35 - 69.80: 13 69.80 - 87.24: 9 Dihedral angle restraints: 3693 sinusoidal: 1426 harmonic: 2267 Sorted by residual: dihedral pdb=" CA LYS A 210 " pdb=" C LYS A 210 " pdb=" N CYS A 211 " pdb=" CA CYS A 211 " ideal model delta harmonic sigma weight residual -180.00 -142.31 -37.69 0 5.00e+00 4.00e-02 5.68e+01 dihedral pdb=" CA VAL A 209 " pdb=" C VAL A 209 " pdb=" N LYS A 210 " pdb=" CA LYS A 210 " ideal model delta harmonic sigma weight residual 180.00 -153.85 -26.15 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA TRP A 283 " pdb=" C TRP A 283 " pdb=" N ALA A 284 " pdb=" CA ALA A 284 " ideal model delta harmonic sigma weight residual 180.00 155.02 24.98 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 3690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 819 0.063 - 0.126: 132 0.126 - 0.188: 17 0.188 - 0.251: 2 0.251 - 0.314: 1 Chirality restraints: 971 Sorted by residual: chirality pdb=" CB VAL B 5 " pdb=" CA VAL B 5 " pdb=" CG1 VAL B 5 " pdb=" CG2 VAL B 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB VAL B 123 " pdb=" CA VAL B 123 " pdb=" CG1 VAL B 123 " pdb=" CG2 VAL B 123 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ASP B 90 " pdb=" N ASP B 90 " pdb=" C ASP B 90 " pdb=" CB ASP B 90 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.94e-01 ... (remaining 968 not shown) Planarity restraints: 1067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 280 " -0.020 2.00e-02 2.50e+03 2.18e-02 1.19e+01 pdb=" CG TRP A 280 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A 280 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 280 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 280 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 280 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 280 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 280 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 280 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 280 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 210 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.93e+00 pdb=" C LYS A 210 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS A 210 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS A 211 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 89 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C ARG B 89 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG B 89 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP B 90 " -0.013 2.00e-02 2.50e+03 ... (remaining 1064 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 76 2.61 - 3.18: 5686 3.18 - 3.75: 9220 3.75 - 4.33: 12704 4.33 - 4.90: 20703 Nonbonded interactions: 48389 Sorted by model distance: nonbonded pdb=" OD1 ASP A 423 " pdb=" OH TYR A 470 " model vdw 2.035 2.440 nonbonded pdb=" NH1 ARG A 322 " pdb=" OE2 GLU A 674 " model vdw 2.122 2.520 nonbonded pdb=" OG1 THR A 533 " pdb=" OD2 ASP B 73 " model vdw 2.206 2.440 nonbonded pdb=" O SER A 321 " pdb=" OG1 THR A 324 " model vdw 2.206 2.440 nonbonded pdb=" OH TYR A 306 " pdb=" OG SER A 633 " model vdw 2.207 2.440 ... (remaining 48384 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 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: 1.640 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: 7.020 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 0.049 6292 Z= 0.324 Angle : 0.841 11.263 8545 Z= 0.481 Chirality : 0.049 0.314 971 Planarity : 0.004 0.043 1067 Dihedral : 14.925 87.244 2231 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.90 % Allowed : 0.75 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.81 (0.31), residues: 777 helix: 0.17 (0.29), residues: 332 sheet: -1.51 (0.40), residues: 166 loop : -2.63 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 280 HIS 0.006 0.001 HIS A 476 PHE 0.019 0.002 PHE A 355 TYR 0.022 0.002 TYR A 121 ARG 0.011 0.001 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 159 time to evaluate : 0.579 Fit side-chains REVERT: A 53 GLU cc_start: 0.8070 (tp30) cc_final: 0.7626 (tp30) REVERT: A 105 ASP cc_start: 0.8431 (m-30) cc_final: 0.8104 (m-30) REVERT: A 147 LEU cc_start: 0.9140 (mm) cc_final: 0.8927 (mm) REVERT: A 228 MET cc_start: 0.8136 (tmm) cc_final: 0.7803 (tmm) REVERT: B 11 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7358 (tt) outliers start: 6 outliers final: 2 residues processed: 165 average time/residue: 0.1715 time to fit residues: 38.1408 Evaluate side-chains 127 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 69.8617 > 50: distance: 5 - 20: 29.193 distance: 15 - 20: 28.962 distance: 20 - 21: 25.441 distance: 21 - 22: 15.623 distance: 21 - 24: 11.884 distance: 22 - 23: 33.764 distance: 22 - 28: 40.082 distance: 24 - 25: 47.263 distance: 25 - 26: 17.589 distance: 25 - 27: 26.996 distance: 29 - 30: 39.423 distance: 30 - 32: 16.195 distance: 32 - 33: 51.855 distance: 33 - 34: 8.518 distance: 33 - 36: 19.706 distance: 34 - 35: 9.722 distance: 34 - 40: 39.585 distance: 36 - 37: 57.488 distance: 37 - 38: 5.367 distance: 38 - 39: 55.736 distance: 41 - 44: 36.709 distance: 42 - 43: 39.555 distance: 42 - 48: 40.475 distance: 44 - 45: 29.353 distance: 44 - 46: 44.687 distance: 45 - 47: 9.233 distance: 48 - 49: 54.555 distance: 49 - 50: 35.842 distance: 49 - 52: 48.535 distance: 50 - 58: 32.415 distance: 52 - 53: 30.035 distance: 53 - 54: 22.611 distance: 53 - 55: 5.186 distance: 54 - 56: 30.096 distance: 55 - 57: 40.739 distance: 56 - 57: 20.390 distance: 58 - 59: 12.934 distance: 58 - 64: 42.942 distance: 59 - 60: 45.055 distance: 59 - 62: 39.305 distance: 60 - 61: 20.695 distance: 60 - 65: 42.941 distance: 62 - 63: 33.676 distance: 63 - 64: 56.902 distance: 65 - 66: 11.478 distance: 66 - 67: 10.939 distance: 66 - 69: 32.808 distance: 67 - 68: 41.693 distance: 67 - 74: 4.521 distance: 69 - 70: 10.637 distance: 70 - 71: 12.104 distance: 71 - 72: 39.569 distance: 71 - 73: 33.536 distance: 74 - 75: 30.488 distance: 74 - 80: 10.193 distance: 75 - 76: 32.918 distance: 75 - 78: 13.046 distance: 76 - 77: 45.110 distance: 76 - 81: 15.311 distance: 78 - 79: 39.327 distance: 79 - 80: 8.639 distance: 81 - 82: 16.427 distance: 82 - 83: 11.055 distance: 82 - 85: 42.569 distance: 83 - 86: 12.299 distance: 86 - 87: 16.700 distance: 87 - 88: 24.810 distance: 87 - 90: 28.778 distance: 88 - 89: 7.193 distance: 88 - 92: 30.027