Starting phenix.real_space_refine (version: dev) on Thu May 12 16:03:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/05_2022/7bh9_12187.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/05_2022/7bh9_12187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/05_2022/7bh9_12187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/05_2022/7bh9_12187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/05_2022/7bh9_12187.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/05_2022/7bh9_12187.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 5876 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4704 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 24, 'TRANS': 560, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "E" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1129 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.92, per 1000 atoms: 0.67 Number of scatterers: 5876 At special positions: 0 Unit cell: (68.77, 81.466, 111.09, 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) Zn 1 29.99 S 34 16.00 O 1084 8.00 N 970 7.00 C 3787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=1.99 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 Links applied NAG-ASN " NAG A 902 " - " ASN A 546 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 53 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 824.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 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: 1372 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 58.1% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.676A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 81 removed outlier: 3.596A pdb=" N ASN A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.009A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 129 removed outlier: 3.507A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.622A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix removed outlier: 3.708A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 221 through 252 removed outlier: 3.799A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 253 through 256 removed outlier: 4.168A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.630A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.837A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.639A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.890A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.993A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 removed outlier: 4.044A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.910A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 481 removed outlier: 3.667A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.536A pdb=" N SER A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.114A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.838A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.895A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.755A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.630A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.988A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'E' and resid 376 through 379 Processing sheet with id=AA5, first strand: chain 'E' and resid 448 through 454 removed outlier: 6.095A pdb=" N TYR E 449 " --> pdb=" O PHE E 497 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N PHE E 497 " --> pdb=" O TYR E 449 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR E 451 " --> pdb=" O TYR E 495 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 271 hydrogen bonds defined for protein. 747 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: 1.69 Time building geometry restraints manager: 2.20 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: 1248 1.33 - 1.45: 1531 1.45 - 1.57: 3206 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 6041 Sorted by residual: bond pdb=" CA SER A 331 " pdb=" CB SER A 331 " ideal model delta sigma weight residual 1.530 1.472 0.058 1.55e-02 4.16e+03 1.40e+01 bond pdb=" C THR E 478 " pdb=" N PRO E 479 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.25e-02 6.40e+03 1.14e+01 bond pdb=" N VAL E 483 " pdb=" CA VAL E 483 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.15e-02 7.56e+03 8.70e+00 bond pdb=" N SER A 331 " pdb=" CA SER A 331 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.22e-02 6.72e+03 6.28e+00 bond pdb=" C GLU A 22 " pdb=" O GLU A 22 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.19e-02 7.06e+03 5.92e+00 ... (remaining 6036 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.59: 182 106.59 - 113.46: 3137 113.46 - 120.33: 2409 120.33 - 127.20: 2388 127.20 - 134.07: 93 Bond angle restraints: 8209 Sorted by residual: angle pdb=" N ASN E 481 " pdb=" CA ASN E 481 " pdb=" C ASN E 481 " ideal model delta sigma weight residual 112.97 104.76 8.21 1.06e+00 8.90e-01 6.00e+01 angle pdb=" N GLY E 482 " pdb=" CA GLY E 482 " pdb=" C GLY E 482 " ideal model delta sigma weight residual 115.30 106.84 8.46 1.39e+00 5.18e-01 3.71e+01 angle pdb=" N PRO E 479 " pdb=" CA PRO E 479 " pdb=" C PRO E 479 " ideal model delta sigma weight residual 111.22 118.06 -6.84 1.40e+00 5.10e-01 2.39e+01 angle pdb=" CA CYS E 480 " pdb=" C CYS E 480 " pdb=" N ASN E 481 " ideal model delta sigma weight residual 115.51 120.83 -5.32 1.24e+00 6.50e-01 1.84e+01 angle pdb=" C ASN A 330 " pdb=" CA ASN A 330 " pdb=" CB ASN A 330 " ideal model delta sigma weight residual 111.02 104.86 6.16 1.62e+00 3.81e-01 1.44e+01 ... (remaining 8204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 3169 16.40 - 32.79: 280 32.79 - 49.19: 50 49.19 - 65.58: 16 65.58 - 81.98: 4 Dihedral angle restraints: 3519 sinusoidal: 1381 harmonic: 2138 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual -86.00 -121.93 35.93 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CA TYR A 252 " pdb=" C TYR A 252 " pdb=" N PRO A 253 " pdb=" CA PRO A 253 " ideal model delta harmonic sigma weight residual -180.00 -161.11 -18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA PRO A 389 " pdb=" C PRO A 389 " pdb=" N PHE A 390 " pdb=" CA PHE A 390 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 656 0.053 - 0.105: 183 0.105 - 0.158: 31 0.158 - 0.210: 1 0.210 - 0.263: 2 Chirality restraints: 873 Sorted by residual: chirality pdb=" CA ASN E 481 " pdb=" N ASN E 481 " pdb=" C ASN E 481 " pdb=" CB ASN E 481 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO E 479 " pdb=" N PRO E 479 " pdb=" C PRO E 479 " pdb=" CB PRO E 479 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB ILE A 21 " pdb=" CA ILE A 21 " pdb=" CG1 ILE A 21 " pdb=" CG2 ILE A 21 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 870 not shown) Planarity restraints: 1049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 495 " 0.023 2.00e-02 2.50e+03 1.35e-02 3.67e+00 pdb=" CG TYR E 495 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR E 495 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR E 495 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 495 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 495 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 495 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 495 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 21 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C ILE A 21 " -0.033 2.00e-02 2.50e+03 pdb=" O ILE A 21 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 22 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " -0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 235 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.026 5.00e-02 4.00e+02 ... (remaining 1046 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 37 2.60 - 3.17: 4671 3.17 - 3.75: 8205 3.75 - 4.32: 12466 4.32 - 4.90: 21205 Nonbonded interactions: 46584 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.021 2.230 nonbonded pdb=" OG SER A 19 " pdb=" OE1 GLU A 23 " model vdw 2.175 2.440 nonbonded pdb=" O SER E 438 " pdb=" OG SER E 438 " model vdw 2.247 2.440 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.284 2.440 nonbonded pdb=" OE2 GLU A 435 " pdb=" NZ LYS A 541 " model vdw 2.289 2.520 ... (remaining 46579 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 34 5.16 5 C 3787 2.51 5 N 970 2.21 5 O 1084 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.760 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: 8.350 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.050 Process input model: 20.630 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 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 : 0.007 0.058 6041 Z= 0.442 Angle : 0.759 8.974 8209 Z= 0.443 Chirality : 0.049 0.263 873 Planarity : 0.005 0.046 1046 Dihedral : 13.233 81.978 2138 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.10 (0.27), residues: 718 helix: -1.42 (0.24), residues: 375 sheet: -2.04 (0.69), residues: 41 loop : -2.83 (0.28), residues: 302 *********************** 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 68 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.761 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 67 average time/residue: 1.0199 time to fit residues: 72.4582 Evaluate side-chains 49 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.609 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0528 time to fit residues: 1.0282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 374 HIS A 380 GLN A 535 HIS E 354 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 6041 Z= 0.149 Angle : 0.492 5.352 8209 Z= 0.262 Chirality : 0.039 0.131 873 Planarity : 0.004 0.032 1046 Dihedral : 4.235 14.543 809 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.30), residues: 718 helix: 0.07 (0.28), residues: 371 sheet: -1.06 (0.66), residues: 49 loop : -2.29 (0.29), residues: 298 *********************** 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 60 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.638 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 1.0277 time to fit residues: 64.5421 Evaluate side-chains 52 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.9404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 chunk 65 optimal weight: 0.2980 chunk 70 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 22 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 6041 Z= 0.145 Angle : 0.459 5.263 8209 Z= 0.241 Chirality : 0.039 0.132 873 Planarity : 0.003 0.031 1046 Dihedral : 3.844 13.219 809 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.64 (0.31), residues: 718 helix: 0.67 (0.28), residues: 379 sheet: -0.40 (0.82), residues: 37 loop : -1.89 (0.30), residues: 302 *********************** 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 58 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.733 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 55 average time/residue: 1.0434 time to fit residues: 61.0800 Evaluate side-chains 52 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.723 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0556 time to fit residues: 1.1579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 6041 Z= 0.197 Angle : 0.484 5.421 8209 Z= 0.255 Chirality : 0.040 0.133 873 Planarity : 0.003 0.030 1046 Dihedral : 3.926 13.783 809 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.33 (0.31), residues: 718 helix: 0.90 (0.28), residues: 380 sheet: -0.32 (0.73), residues: 47 loop : -1.74 (0.32), residues: 291 *********************** 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 58 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.695 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 1.1192 time to fit residues: 65.3814 Evaluate side-chains 53 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.599 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0514 time to fit residues: 0.9321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 6041 Z= 0.300 Angle : 0.534 5.561 8209 Z= 0.283 Chirality : 0.042 0.142 873 Planarity : 0.004 0.033 1046 Dihedral : 4.150 15.199 809 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.34 (0.31), residues: 718 helix: 0.87 (0.28), residues: 382 sheet: -0.32 (0.72), residues: 49 loop : -1.74 (0.32), residues: 287 *********************** REFINEMENT MACRO_CYCLE 5 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 57 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.706 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 55 average time/residue: 1.1466 time to fit residues: 66.7485 Evaluate side-chains 53 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.701 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0517 time to fit residues: 1.0105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 6041 Z= 0.178 Angle : 0.475 5.423 8209 Z= 0.250 Chirality : 0.040 0.133 873 Planarity : 0.003 0.030 1046 Dihedral : 3.925 13.446 809 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.04 (0.32), residues: 718 helix: 1.11 (0.28), residues: 381 sheet: -0.07 (0.75), residues: 47 loop : -1.59 (0.32), residues: 290 *********************** REFINEMENT MACRO_CYCLE 6 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 60 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.697 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 57 average time/residue: 1.1774 time to fit residues: 70.8173 Evaluate side-chains 54 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.689 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0523 time to fit residues: 1.0216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 6041 Z= 0.139 Angle : 0.449 5.357 8209 Z= 0.234 Chirality : 0.039 0.131 873 Planarity : 0.003 0.030 1046 Dihedral : 3.683 13.093 809 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.35 (0.32), residues: 718 helix: 1.50 (0.29), residues: 374 sheet: 0.48 (0.90), residues: 37 loop : -1.46 (0.32), residues: 307 *********************** REFINEMENT MACRO_CYCLE 7 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 62 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.703 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 61 average time/residue: 1.1328 time to fit residues: 73.0979 Evaluate side-chains 57 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0527 time to fit residues: 1.0333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 0.0050 chunk 64 optimal weight: 10.0000 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 6041 Z= 0.129 Angle : 0.456 7.216 8209 Z= 0.235 Chirality : 0.038 0.129 873 Planarity : 0.003 0.030 1046 Dihedral : 3.578 13.124 809 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.55 (0.32), residues: 718 helix: 1.64 (0.29), residues: 373 sheet: 0.71 (0.91), residues: 37 loop : -1.34 (0.32), residues: 308 *********************** REFINEMENT MACRO_CYCLE 8 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 67 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.615 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 1.0249 time to fit residues: 69.6084 Evaluate side-chains 60 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.706 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.1837 time to fit residues: 1.1704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 0.0040 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 6041 Z= 0.123 Angle : 0.451 6.597 8209 Z= 0.230 Chirality : 0.038 0.129 873 Planarity : 0.003 0.030 1046 Dihedral : 3.469 12.903 809 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.73 (0.32), residues: 718 helix: 1.77 (0.29), residues: 371 sheet: 0.85 (0.93), residues: 37 loop : -1.21 (0.33), residues: 310 *********************** REFINEMENT MACRO_CYCLE 9 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 65 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.743 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 65 average time/residue: 1.1583 time to fit residues: 80.0506 Evaluate side-chains 57 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.0441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 0.0070 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 17 optimal weight: 6.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 6041 Z= 0.138 Angle : 0.467 8.987 8209 Z= 0.238 Chirality : 0.039 0.128 873 Planarity : 0.003 0.029 1046 Dihedral : 3.502 13.118 809 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.80 (0.32), residues: 718 helix: 1.77 (0.29), residues: 372 sheet: 0.88 (0.93), residues: 37 loop : -1.11 (0.34), residues: 309 ********************** REFINEMENT MACRO_CYCLE 10 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 59 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.696 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 59 average time/residue: 1.0676 time to fit residues: 66.9059 Evaluate side-chains 57 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.8829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.095816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.080178 restraints weight = 10089.656| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.79 r_work: 0.3058 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work: 0.3041 rms_B_bonded: 2.60 restraints_weight: 0.1250 r_work: 0.3033 rms_B_bonded: 2.64 restraints_weight: 0.0625 r_work: 0.3024 rms_B_bonded: 2.70 restraints_weight: 0.0312 r_work: 0.3015 rms_B_bonded: 2.77 restraints_weight: 0.0156 r_work: 0.3005 rms_B_bonded: 2.86 restraints_weight: 0.0078 r_work: 0.2996 rms_B_bonded: 2.96 restraints_weight: 0.0039 r_work: 0.2986 rms_B_bonded: 3.07 restraints_weight: 0.0020 r_work: 0.2976 rms_B_bonded: 3.20 restraints_weight: 0.0010 r_work: 0.2966 rms_B_bonded: 3.35 restraints_weight: 0.0005 r_work: 0.2955 rms_B_bonded: 3.50 restraints_weight: 0.0002 r_work: 0.2944 rms_B_bonded: 3.68 restraints_weight: 0.0001 r_work: 0.2933 rms_B_bonded: 3.87 restraints_weight: 0.0001 r_work: 0.2921 rms_B_bonded: 4.07 restraints_weight: 0.0000 r_work: 0.2909 rms_B_bonded: 4.29 restraints_weight: 0.0000 r_work: 0.2896 rms_B_bonded: 4.53 restraints_weight: 0.0000 r_work: 0.2883 rms_B_bonded: 4.79 restraints_weight: 0.0000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 6041 Z= 0.145 Angle : 0.467 6.794 8209 Z= 0.239 Chirality : 0.039 0.128 873 Planarity : 0.003 0.029 1046 Dihedral : 3.551 14.190 809 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.84 (0.33), residues: 718 helix: 1.79 (0.29), residues: 372 sheet: 0.93 (0.93), residues: 37 loop : -1.06 (0.34), residues: 309 =============================================================================== Job complete usr+sys time: 1939.67 seconds wall clock time: 35 minutes 7.32 seconds (2107.32 seconds total)