Starting phenix.real_space_refine on Sun May 19 16:32:00 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1f_18809.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1f_18809.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True resolution=3.67 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1f_18809.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1f_18809.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1f_18809.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8r1f_18809.map" } resolution = 3.67 refinement { run = *minimization_global rigid_body local_grid_search morphing \ simulated_annealing adp occupancy nqh_flips } pdb_interpretation { c_beta_restraints = False ramachandran_plot_restraints { enabled = False } } 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= 0.031 sd= 0.268 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: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 5307 2.51 5 N 1431 2.21 5 O 1577 1.98 5 H 8296 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 16668 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 11116 Inner-chain residues flagged as termini: ['pdbres="PHE A 167 "', 'pdbres="VAL A 234 "'] Classifications: {'peptide': 681} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 28, 'TRANS': 652} Chain breaks: 1 Chain: "B" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2394 Classifications: {'peptide': 142} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "C" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3158 Classifications: {'peptide': 202} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 186} Time building chain proxies: 5.20, per 1000 atoms: 0.31 Number of scatterers: 16668 At special positions: 0 Unit cell: (118.44, 110.88, 109.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 1577 8.00 N 1431 7.00 C 5307 6.00 H 8296 1.00 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: 8.34 Conformation dependent library (CDL) restraints added in 909.6 milliseconds Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 47.8% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 130 through 142 removed outlier: 3.769A pdb=" N ILE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 236 through 248 removed outlier: 4.536A pdb=" N SER A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 273 removed outlier: 3.517A pdb=" N TYR A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 276 through 279 No H-bonds generated for 'chain 'A' and resid 276 through 279' Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.916A pdb=" N LEU A 284 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU A 292 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 297 removed outlier: 4.465A pdb=" N HIS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 294 through 297' Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 305 through 315 removed outlier: 4.011A pdb=" N LYS A 315 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 330 removed outlier: 4.230A pdb=" N LYS A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 353 removed outlier: 3.536A pdb=" N LEU A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 366 through 385 Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 477 through 483 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 486 through 515 Processing helix chain 'A' and resid 532 through 546 Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 569 through 583 Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 609 through 624 Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 648 through 654 removed outlier: 3.506A pdb=" N GLY A 652 " --> pdb=" O ARG A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 667 removed outlier: 3.626A pdb=" N SER A 661 " --> pdb=" O VAL A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 710 through 722 Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.926A pdb=" N ALA A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 749 Processing helix chain 'A' and resid 752 through 760 removed outlier: 3.583A pdb=" N LEU A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 773 Processing helix chain 'A' and resid 785 through 796 Processing helix chain 'A' and resid 799 through 810 Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 855 through 868 Processing helix chain 'B' and resid 19 through 25 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 92 through 99 Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 144 through 147 No H-bonds generated for 'chain 'B' and resid 144 through 147' Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 177 through 180 No H-bonds generated for 'chain 'C' and resid 177 through 180' Processing helix chain 'C' and resid 278 through 291 Processing sheet with id= A, first strand: chain 'A' and resid 522 through 527 removed outlier: 6.321A pdb=" N GLN A 554 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU A 525 " --> pdb=" O GLN A 554 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR A 556 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL A 527 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLU A 558 " --> pdb=" O VAL A 527 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 590 through 593 removed outlier: 3.634A pdb=" N LEU A 598 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 681 through 685 Processing sheet with id= D, first strand: chain 'A' and resid 775 through 777 Processing sheet with id= E, first strand: chain 'B' and resid 60 through 62 Processing sheet with id= F, first strand: chain 'B' and resid 89 through 91 Processing sheet with id= G, first strand: chain 'C' and resid 110 through 113 removed outlier: 4.523A pdb=" N HIS C 233 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 124 through 127 removed outlier: 8.702A pdb=" N MET C 133 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU C 271 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N CYS C 135 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG C 273 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU C 257 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG C 267 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE C 255 " --> pdb=" O ARG C 267 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER C 269 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR C 253 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU C 271 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE C 251 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA C 161 " --> pdb=" O HIS C 214 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N HIS C 214 " --> pdb=" O ALA C 161 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 942 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: 6.45 Time building geometry restraints manager: 7.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 8267 1.15 - 1.31: 1437 1.31 - 1.48: 3387 1.48 - 1.65: 3669 1.65 - 1.81: 85 Bond restraints: 16845 Sorted by residual: bond pdb=" N LEU A 849 " pdb=" H LEU A 849 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" N ASN A 258 " pdb=" H ASN A 258 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" N ASP A 389 " pdb=" H ASP A 389 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" N LYS B 115 " pdb=" H LYS B 115 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" N PHE A 612 " pdb=" H PHE A 612 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.62e+01 ... (remaining 16840 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.92: 202 105.92 - 112.92: 19472 112.92 - 119.93: 4806 119.93 - 126.93: 5855 126.93 - 133.94: 83 Bond angle restraints: 30418 Sorted by residual: angle pdb=" C PRO A 745 " pdb=" N LEU A 746 " pdb=" CA LEU A 746 " ideal model delta sigma weight residual 120.79 123.38 -2.59 1.39e+00 5.18e-01 3.49e+00 angle pdb=" CA TYR A 494 " pdb=" CB TYR A 494 " pdb=" CG TYR A 494 " ideal model delta sigma weight residual 113.90 117.05 -3.15 1.80e+00 3.09e-01 3.06e+00 angle pdb=" CA VAL A 740 " pdb=" C VAL A 740 " pdb=" N THR A 741 " ideal model delta sigma weight residual 116.60 119.07 -2.47 1.45e+00 4.76e-01 2.90e+00 angle pdb=" CA TRP A 791 " pdb=" CB TRP A 791 " pdb=" CG TRP A 791 " ideal model delta sigma weight residual 113.60 110.52 3.08 1.90e+00 2.77e-01 2.63e+00 angle pdb=" CB ARG C 196 " pdb=" CG ARG C 196 " pdb=" CD ARG C 196 " ideal model delta sigma weight residual 111.30 114.94 -3.64 2.30e+00 1.89e-01 2.50e+00 ... (remaining 30413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 5435 17.29 - 34.58: 379 34.58 - 51.87: 132 51.87 - 69.16: 33 69.16 - 86.45: 5 Dihedral angle restraints: 5984 sinusoidal: 4370 harmonic: 1614 Sorted by residual: dihedral pdb=" CA ARG C 209 " pdb=" CB ARG C 209 " pdb=" CG ARG C 209 " pdb=" CD ARG C 209 " ideal model delta sinusoidal sigma weight residual 60.00 117.00 -57.00 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " pdb=" CG ARG A 155 " pdb=" CD ARG A 155 " ideal model delta sinusoidal sigma weight residual -60.00 -114.03 54.03 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA ARG A 529 " pdb=" CB ARG A 529 " pdb=" CG ARG A 529 " pdb=" CD ARG A 529 " ideal model delta sinusoidal sigma weight residual -180.00 -128.92 -51.08 3 1.50e+01 4.44e-03 8.97e+00 ... (remaining 5981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 834 0.031 - 0.061: 302 0.061 - 0.092: 70 0.092 - 0.122: 45 0.122 - 0.153: 9 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA ILE B 34 " pdb=" N ILE B 34 " pdb=" C ILE B 34 " pdb=" CB ILE B 34 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE A 444 " pdb=" N ILE A 444 " pdb=" C ILE A 444 " pdb=" CB ILE A 444 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA VAL C 157 " pdb=" N VAL C 157 " pdb=" C VAL C 157 " pdb=" CB VAL C 157 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 1257 not shown) Planarity restraints: 2476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 306 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 307 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 734 " -0.131 9.50e-02 1.11e+02 4.38e-02 2.10e+00 pdb=" NE ARG A 734 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 734 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 734 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 734 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 734 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 141 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.49e+00 pdb=" N PRO C 142 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " 0.017 5.00e-02 4.00e+02 ... (remaining 2473 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 569 2.06 - 2.70: 23954 2.70 - 3.33: 49695 3.33 - 3.97: 63435 3.97 - 4.60: 95280 Nonbonded interactions: 232933 Sorted by model distance: nonbonded pdb="HE21 GLN A 410 " pdb=" O GLU A 415 " model vdw 1.429 1.850 nonbonded pdb=" H SER B 118 " pdb=" OE1 GLU B 121 " model vdw 1.480 1.850 nonbonded pdb=" O LEU A 770 " pdb=" HG1 THR A 774 " model vdw 1.523 1.850 nonbonded pdb=" O GLY A 154 " pdb=" HG SER A 158 " model vdw 1.563 1.850 nonbonded pdb=" OE1 GLU A 860 " pdb=" HE ARG A 861 " model vdw 1.571 1.850 ... (remaining 232928 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: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.50 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined 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: 0.030 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: 0.160 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.070 Process input model: 31.970 Find NCS groups from input model: 0.190 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:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:22.360 Internal consistency checks: 0.000 Total: 55.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5396 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 : 0.002 0.019 8549 Z= 0.143 Angle : 0.506 3.884 11554 Z= 0.281 Chirality : 0.038 0.153 1260 Planarity : 0.005 0.057 1505 Dihedral : 10.847 77.471 3280 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.32 % Allowed : 2.34 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.25), residues: 1017 helix: -0.35 (0.21), residues: 483 sheet: -0.55 (0.47), residues: 117 loop : -0.04 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 267 TYR 0.016 0.001 TYR A 494 PHE 0.018 0.002 PHE A 730 TRP 0.011 0.002 TRP A 791 HIS 0.004 0.001 HIS C 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5549 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8549 Z= 0.333 Angle : 0.625 5.196 11554 Z= 0.337 Chirality : 0.054 0.223 1260 Planarity : 0.005 0.063 1505 Dihedral : 10.663 69.537 3280 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.69 % Favored : 92.82 % Rotamer: Outliers : 0.42 % Allowed : 2.87 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.26 (0.22), residues: 1017 helix: -2.27 (0.19), residues: 482 sheet: -2.04 (0.46), residues: 118 loop : -1.81 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 500 TYR 0.017 0.002 TYR A 624 PHE 0.021 0.002 PHE A 730 TRP 0.013 0.002 TRP A 600 HIS 0.005 0.001 HIS B 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 64 optimal weight: 50.0000 chunk 17 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 96 optimal weight: 30.0000 chunk 12 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 30.0000 chunk 68 optimal weight: 10.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5634 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 8549 Z= 0.434 Angle : 0.657 5.699 11554 Z= 0.361 Chirality : 0.056 0.232 1260 Planarity : 0.006 0.072 1505 Dihedral : 11.887 75.643 3280 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 2.46 % Allowed : 12.29 % Favored : 85.25 % Rotamer: Outliers : 1.27 % Allowed : 5.63 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.47 (0.21), residues: 1017 helix: -2.82 (0.17), residues: 476 sheet: -2.68 (0.48), residues: 106 loop : -3.07 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 196 TYR 0.017 0.002 TYR A 748 PHE 0.021 0.002 PHE A 256 TRP 0.010 0.002 TRP B 139 HIS 0.007 0.001 HIS A 297 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 90 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 60 optimal weight: 70.0000 chunk 71 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5607 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8549 Z= 0.247 Angle : 0.523 4.533 11554 Z= 0.282 Chirality : 0.052 0.227 1260 Planarity : 0.005 0.059 1505 Dihedral : 11.352 72.614 3280 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 1.08 % Allowed : 10.91 % Favored : 88.00 % Rotamer: Outliers : 0.85 % Allowed : 5.20 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.12 (0.21), residues: 1017 helix: -2.48 (0.18), residues: 476 sheet: -2.61 (0.50), residues: 96 loop : -2.95 (0.24), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 734 TYR 0.014 0.001 TYR A 494 PHE 0.015 0.002 PHE A 256 TRP 0.010 0.001 TRP B 139 HIS 0.004 0.001 HIS A 297 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 60.0000 chunk 56 optimal weight: 4.9990 chunk 66 optimal weight: 110.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5644 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8549 Z= 0.353 Angle : 0.593 4.763 11554 Z= 0.323 Chirality : 0.054 0.225 1260 Planarity : 0.005 0.066 1505 Dihedral : 11.663 85.049 3280 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 2.16 % Allowed : 13.37 % Favored : 84.46 % Rotamer: Outliers : 2.02 % Allowed : 5.63 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.80 (0.20), residues: 1017 helix: -2.89 (0.17), residues: 474 sheet: -3.32 (0.46), residues: 96 loop : -3.40 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 138 TYR 0.017 0.002 TYR A 659 PHE 0.016 0.002 PHE A 256 TRP 0.009 0.002 TRP B 139 HIS 0.005 0.001 HIS A 297 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 1 optimal weight: 30.0000 chunk 11 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 51 optimal weight: 40.0000 chunk 90 optimal weight: 30.0000 chunk 100 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 overall best weight: 8.1994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5654 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8549 Z= 0.339 Angle : 0.584 5.670 11554 Z= 0.318 Chirality : 0.054 0.236 1260 Planarity : 0.005 0.063 1505 Dihedral : 12.096 77.734 3280 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 2.46 % Allowed : 15.44 % Favored : 82.10 % Rotamer: Outliers : 2.65 % Allowed : 6.58 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.96 (0.21), residues: 1017 helix: -2.90 (0.18), residues: 474 sheet: -3.74 (0.42), residues: 102 loop : -3.54 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 155 TYR 0.016 0.002 TYR B 86 PHE 0.015 0.002 PHE A 256 TRP 0.012 0.002 TRP B 139 HIS 0.006 0.001 HIS A 297 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 385.27 seconds wall clock time: 7 minutes 27.10 seconds (447.10 seconds total)