Starting phenix.real_space_refine on Wed Sep 25 17:38:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yo0_10862/09_2024/6yo0_10862_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yo0_10862/09_2024/6yo0_10862.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/6yo0_10862/09_2024/6yo0_10862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yo0_10862/09_2024/6yo0_10862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yo0_10862/09_2024/6yo0_10862_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yo0_10862/09_2024/6yo0_10862_trim.cif" } resolution = 2.9 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= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 101 5.16 5 C 17412 2.51 5 N 4798 2.21 5 O 5349 1.98 5 H 28102 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "F1 ARG 375": not complete - not flipped Time to flip 146 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 55780 Number of models: 1 Model: "" Number of chains: 17 Chain: "G1" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 3000 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain: "g1" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1420 Classifications: {'peptide': 90} Link IDs: {'TRANS': 89} Chain breaks: 1 Chain: "C1" Number of atoms: 7980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 7980 Classifications: {'peptide': 513} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 495} Chain: "D1" Number of atoms: 7135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 7135 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "B1" Number of atoms: 7934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 7934 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 493} Chain: "F1" Number of atoms: 7112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7112 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 23, 'TRANS': 445} Chain: "A1" Number of atoms: 7946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 7946 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 494} Chain: "E1" Number of atoms: 7135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 7135 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "i1" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 638 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "s" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 486 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "b" Number of atoms: 3227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3227 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 3, 'TRANS': 201} Chain breaks: 1 Chain: "d" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1615 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "C1" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B1" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A1" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.47, per 1000 atoms: 0.42 Number of scatterers: 55780 At special positions: 0 Unit cell: (135.29, 157.7, 148.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 13 15.00 Mg 5 11.99 O 5349 8.00 N 4798 7.00 C 17412 6.00 H 28102 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.46 Conformation dependent library (CDL) restraints added in 3.5 seconds 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6584 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 0 sheets defined 45.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'G1' and resid 43 through 57 Processing helix chain 'G1' and resid 62 through 77 Processing helix chain 'G1' and resid 79 through 86 Processing helix chain 'G1' and resid 92 through 102 Processing helix chain 'G1' and resid 109 through 120 Processing helix chain 'G1' and resid 124 through 141 Proline residue: G1 128 - end of helix Processing helix chain 'G1' and resid 157 through 171 Processing helix chain 'G1' and resid 203 through 215 Processing helix chain 'g1' and resid 26 through 60 Processing helix chain 'g1' and resid 248 through 297 Processing helix chain 'C1' and resid 40 through 48 Processing helix chain 'C1' and resid 182 through 187 Processing helix chain 'C1' and resid 206 through 223 removed outlier: 3.948A pdb=" N LYSC1 218 " --> pdb=" O ILEC1 214 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLUC1 219 " --> pdb=" O LEUC1 215 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ALAC1 220 " --> pdb=" O ASNC1 216 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHEC1 221 " --> pdb=" O GLNC1 217 " (cutoff:3.500A) Processing helix chain 'C1' and resid 241 through 253 Processing helix chain 'C1' and resid 271 through 290 Proline residue: C1 278 - end of helix removed outlier: 4.018A pdb=" N PHEC1 288 " --> pdb=" O ILEC1 284 " (cutoff:3.500A) Processing helix chain 'C1' and resid 302 through 315 Processing helix chain 'C1' and resid 322 through 324 No H-bonds generated for 'chain 'C1' and resid 322 through 324' Processing helix chain 'C1' and resid 329 through 339 removed outlier: 3.871A pdb=" N LEUC1 336 " --> pdb=" O LEUC1 332 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARGC1 339 " --> pdb=" O ARGC1 335 " (cutoff:3.500A) Processing helix chain 'C1' and resid 368 through 376 Processing helix chain 'C1' and resid 385 through 389 Processing helix chain 'C1' and resid 406 through 408 No H-bonds generated for 'chain 'C1' and resid 406 through 408' Processing helix chain 'C1' and resid 412 through 434 removed outlier: 4.417A pdb=" N LYSC1 416 " --> pdb=" O LYSC1 412 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILEC1 417 " --> pdb=" O ALAC1 413 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASNC1 420 " --> pdb=" O LYSC1 416 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALAC1 433 " --> pdb=" O ARGC1 429 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N PHEC1 434 " --> pdb=" O GLUC1 430 " (cutoff:3.500A) Processing helix chain 'C1' and resid 446 through 459 Processing helix chain 'C1' and resid 469 through 481 Processing helix chain 'C1' and resid 483 through 485 No H-bonds generated for 'chain 'C1' and resid 483 through 485' Processing helix chain 'C1' and resid 489 through 505 removed outlier: 4.782A pdb=" N LEUC1 493 " --> pdb=" O SERC1 490 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARGC1 504 " --> pdb=" O GLUC1 501 " (cutoff:3.500A) Processing helix chain 'C1' and resid 508 through 517 Processing helix chain 'C1' and resid 522 through 538 Proline residue: C1 533 - end of helix Processing helix chain 'D1' and resid 107 through 109 No H-bonds generated for 'chain 'D1' and resid 107 through 109' Processing helix chain 'D1' and resid 157 through 162 Processing helix chain 'D1' and resid 181 through 192 Processing helix chain 'D1' and resid 209 through 221 Processing helix chain 'D1' and resid 251 through 264 Processing helix chain 'D1' and resid 278 through 291 removed outlier: 3.587A pdb=" N VALD1 287 " --> pdb=" O ALAD1 283 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALAD1 289 " --> pdb=" O SERD1 285 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEUD1 290 " --> pdb=" O GLUD1 286 " (cutoff:3.500A) Processing helix chain 'D1' and resid 304 through 312 removed outlier: 3.667A pdb=" N LEUD1 311 " --> pdb=" O ASPD1 307 " (cutoff:3.500A) Processing helix chain 'D1' and resid 332 through 334 No H-bonds generated for 'chain 'D1' and resid 332 through 334' Processing helix chain 'D1' and resid 339 through 347 removed outlier: 4.342A pdb=" N ALAD1 346 " --> pdb=" O ALAD1 342 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HISD1 347 " --> pdb=" O THRD1 343 " (cutoff:3.500A) Processing helix chain 'D1' and resid 356 through 361 Processing helix chain 'D1' and resid 384 through 410 removed outlier: 4.485A pdb=" N ASPD1 405 " --> pdb=" O LYSD1 401 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILED1 406 " --> pdb=" O SERD1 402 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILED1 409 " --> pdb=" O ASPD1 405 " (cutoff:3.500A) Processing helix chain 'D1' and resid 417 through 432 Processing helix chain 'D1' and resid 438 through 444 removed outlier: 4.843A pdb=" N VALD1 442 " --> pdb=" O METD1 439 " (cutoff:3.500A) Processing helix chain 'D1' and resid 453 through 464 Processing helix chain 'D1' and resid 473 through 475 No H-bonds generated for 'chain 'D1' and resid 473 through 475' Processing helix chain 'D1' and resid 482 through 495 Processing helix chain 'B1' and resid 36 through 49 removed outlier: 3.802A pdb=" N ALAB1 39 " --> pdb=" O THRB1 36 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYB1 49 " --> pdb=" O LYSB1 46 " (cutoff:3.500A) Processing helix chain 'B1' and resid 110 through 112 No H-bonds generated for 'chain 'B1' and resid 110 through 112' Processing helix chain 'B1' and resid 132 through 134 No H-bonds generated for 'chain 'B1' and resid 132 through 134' Processing helix chain 'B1' and resid 182 through 187 Processing helix chain 'B1' and resid 206 through 223 removed outlier: 4.155A pdb=" N ALAB1 210 " --> pdb=" O LYSB1 206 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYSB1 218 " --> pdb=" O ILEB1 214 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLUB1 219 " --> pdb=" O LEUB1 215 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALAB1 220 " --> pdb=" O ASNB1 216 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHEB1 221 " --> pdb=" O GLNB1 217 " (cutoff:3.500A) Processing helix chain 'B1' and resid 241 through 253 Processing helix chain 'B1' and resid 271 through 290 Proline residue: B1 278 - end of helix removed outlier: 3.984A pdb=" N PHEB1 288 " --> pdb=" O ILEB1 284 " (cutoff:3.500A) Processing helix chain 'B1' and resid 302 through 316 Processing helix chain 'B1' and resid 322 through 324 No H-bonds generated for 'chain 'B1' and resid 322 through 324' Processing helix chain 'B1' and resid 329 through 339 removed outlier: 4.015A pdb=" N LEUB1 336 " --> pdb=" O LEUB1 332 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARGB1 339 " --> pdb=" O ARGB1 335 " (cutoff:3.500A) Processing helix chain 'B1' and resid 368 through 376 Processing helix chain 'B1' and resid 385 through 389 Processing helix chain 'B1' and resid 406 through 408 No H-bonds generated for 'chain 'B1' and resid 406 through 408' Processing helix chain 'B1' and resid 412 through 437 removed outlier: 4.071A pdb=" N LYSB1 416 " --> pdb=" O LYSB1 412 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILEB1 417 " --> pdb=" O ALAB1 413 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASNB1 420 " --> pdb=" O LYSB1 416 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALAB1 433 " --> pdb=" O ARGB1 429 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHEB1 434 " --> pdb=" O GLUB1 430 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SERB1 435 " --> pdb=" O LEUB1 431 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLNB1 436 " --> pdb=" O ALAB1 432 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHEB1 437 " --> pdb=" O ALAB1 433 " (cutoff:3.500A) Processing helix chain 'B1' and resid 446 through 459 Processing helix chain 'B1' and resid 469 through 480 Processing helix chain 'B1' and resid 483 through 485 No H-bonds generated for 'chain 'B1' and resid 483 through 485' Processing helix chain 'B1' and resid 489 through 506 removed outlier: 5.014A pdb=" N LEUB1 493 " --> pdb=" O SERB1 490 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARGB1 504 " --> pdb=" O GLUB1 501 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASNB1 506 " --> pdb=" O VALB1 503 " (cutoff:3.500A) Processing helix chain 'B1' and resid 508 through 517 Processing helix chain 'B1' and resid 522 through 538 Proline residue: B1 533 - end of helix Processing helix chain 'F1' and resid 107 through 109 No H-bonds generated for 'chain 'F1' and resid 107 through 109' Processing helix chain 'F1' and resid 157 through 162 Processing helix chain 'F1' and resid 181 through 194 Processing helix chain 'F1' and resid 209 through 218 Processing helix chain 'F1' and resid 247 through 264 removed outlier: 4.660A pdb=" N GLYF1 252 " --> pdb=" O ARGF1 248 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEUF1 253 " --> pdb=" O ALAF1 249 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHEF1 262 " --> pdb=" O VALF1 258 " (cutoff:3.500A) Processing helix chain 'F1' and resid 277 through 291 Processing helix chain 'F1' and resid 304 through 314 removed outlier: 4.079A pdb=" N LEUF1 311 " --> pdb=" O ASPF1 307 " (cutoff:3.500A) Processing helix chain 'F1' and resid 332 through 334 No H-bonds generated for 'chain 'F1' and resid 332 through 334' Processing helix chain 'F1' and resid 339 through 345 Processing helix chain 'F1' and resid 356 through 360 Processing helix chain 'F1' and resid 384 through 407 Processing helix chain 'F1' and resid 417 through 432 Processing helix chain 'F1' and resid 441 through 444 No H-bonds generated for 'chain 'F1' and resid 441 through 444' Processing helix chain 'F1' and resid 453 through 465 Processing helix chain 'F1' and resid 473 through 475 No H-bonds generated for 'chain 'F1' and resid 473 through 475' Processing helix chain 'F1' and resid 482 through 495 Processing helix chain 'A1' and resid 36 through 48 Processing helix chain 'A1' and resid 182 through 187 Processing helix chain 'A1' and resid 206 through 222 removed outlier: 3.721A pdb=" N ALAA1 210 " --> pdb=" O LYSA1 206 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYSA1 218 " --> pdb=" O ILEA1 214 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLUA1 219 " --> pdb=" O LEUA1 215 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALAA1 220 " --> pdb=" O ASNA1 216 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHEA1 221 " --> pdb=" O GLNA1 217 " (cutoff:3.500A) Processing helix chain 'A1' and resid 226 through 228 No H-bonds generated for 'chain 'A1' and resid 226 through 228' Processing helix chain 'A1' and resid 241 through 253 Processing helix chain 'A1' and resid 271 through 290 Proline residue: A1 278 - end of helix removed outlier: 3.946A pdb=" N PHEA1 288 " --> pdb=" O ILEA1 284 " (cutoff:3.500A) Processing helix chain 'A1' and resid 302 through 314 Processing helix chain 'A1' and resid 322 through 324 No H-bonds generated for 'chain 'A1' and resid 322 through 324' Processing helix chain 'A1' and resid 329 through 339 removed outlier: 4.074A pdb=" N ARGA1 339 " --> pdb=" O ARGA1 335 " (cutoff:3.500A) Processing helix chain 'A1' and resid 345 through 347 No H-bonds generated for 'chain 'A1' and resid 345 through 347' Processing helix chain 'A1' and resid 368 through 376 Processing helix chain 'A1' and resid 385 through 389 Processing helix chain 'A1' and resid 406 through 408 No H-bonds generated for 'chain 'A1' and resid 406 through 408' Processing helix chain 'A1' and resid 412 through 438 removed outlier: 3.742A pdb=" N LYSA1 416 " --> pdb=" O LYSA1 412 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILEA1 417 " --> pdb=" O ALAA1 413 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASNA1 420 " --> pdb=" O LYSA1 416 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALAA1 433 " --> pdb=" O ARGA1 429 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHEA1 434 " --> pdb=" O GLUA1 430 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLNA1 436 " --> pdb=" O ALAA1 432 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHEA1 437 " --> pdb=" O ALAA1 433 " (cutoff:3.500A) Processing helix chain 'A1' and resid 443 through 459 Processing helix chain 'A1' and resid 469 through 480 Processing helix chain 'A1' and resid 483 through 485 No H-bonds generated for 'chain 'A1' and resid 483 through 485' Processing helix chain 'A1' and resid 489 through 506 removed outlier: 4.711A pdb=" N LEUA1 493 " --> pdb=" O SERA1 490 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASNA1 506 " --> pdb=" O VALA1 503 " (cutoff:3.500A) Processing helix chain 'A1' and resid 509 through 517 Processing helix chain 'A1' and resid 522 through 538 Proline residue: A1 533 - end of helix Processing helix chain 'E1' and resid 107 through 109 No H-bonds generated for 'chain 'E1' and resid 107 through 109' Processing helix chain 'E1' and resid 157 through 162 Processing helix chain 'E1' and resid 181 through 191 Processing helix chain 'E1' and resid 209 through 222 Processing helix chain 'E1' and resid 251 through 264 removed outlier: 3.665A pdb=" N PHEE1 262 " --> pdb=" O VALE1 258 " (cutoff:3.500A) Processing helix chain 'E1' and resid 278 through 291 removed outlier: 3.830A pdb=" N ALAE1 289 " --> pdb=" O SERE1 285 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEUE1 290 " --> pdb=" O GLUE1 286 " (cutoff:3.500A) Processing helix chain 'E1' and resid 304 through 312 Processing helix chain 'E1' and resid 332 through 334 No H-bonds generated for 'chain 'E1' and resid 332 through 334' Processing helix chain 'E1' and resid 339 through 347 removed outlier: 4.188A pdb=" N ALAE1 346 " --> pdb=" O ALAE1 342 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N HISE1 347 " --> pdb=" O THRE1 343 " (cutoff:3.500A) Processing helix chain 'E1' and resid 356 through 361 Processing helix chain 'E1' and resid 384 through 409 removed outlier: 3.614A pdb=" N LEUE1 403 " --> pdb=" O ASPE1 399 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASPE1 405 " --> pdb=" O LYSE1 401 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ILEE1 406 " --> pdb=" O SERE1 402 " (cutoff:3.500A) Processing helix chain 'E1' and resid 417 through 433 Processing helix chain 'E1' and resid 441 through 444 No H-bonds generated for 'chain 'E1' and resid 441 through 444' Processing helix chain 'E1' and resid 453 through 465 Processing helix chain 'E1' and resid 473 through 476 Processing helix chain 'E1' and resid 482 through 495 Processing helix chain 'i1' and resid 30 through 61 Processing helix chain 's' and resid 116 through 127 removed outlier: 3.595A pdb=" N TYR s 127 " --> pdb=" O ASP s 123 " (cutoff:3.500A) Processing helix chain 's' and resid 130 through 141 Processing helix chain 'b' and resid 28 through 59 removed outlier: 4.093A pdb=" N ALA b 46 " --> pdb=" O ALA b 42 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE b 47 " --> pdb=" O SER b 43 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN b 48 " --> pdb=" O VAL b 44 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN b 49 " --> pdb=" O ALA b 45 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG b 50 " --> pdb=" O ALA b 46 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE b 51 " --> pdb=" O PHE b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 214 through 275 removed outlier: 3.614A pdb=" N LEU b 245 " --> pdb=" O ALA b 241 " (cutoff:3.500A) Processing helix chain 'b' and resid 281 through 296 Processing helix chain 'b' and resid 306 through 322 Processing helix chain 'b' and resid 326 through 332 removed outlier: 4.008A pdb=" N ALA b 331 " --> pdb=" O ALA b 327 " (cutoff:3.500A) Processing helix chain 'b' and resid 338 through 357 removed outlier: 3.681A pdb=" N ILE b 344 " --> pdb=" O GLN b 340 " (cutoff:3.500A) Processing helix chain 'b' and resid 370 through 377 Processing helix chain 'd' and resid 35 through 47 removed outlier: 3.789A pdb=" N ILE d 41 " --> pdb=" O ILE d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 68 Processing helix chain 'd' and resid 80 through 86 Processing helix chain 'd' and resid 92 through 105 Processing helix chain 'd' and resid 110 through 119 Processing helix chain 'd' and resid 123 through 130 1030 hydrogen bonds defined for protein. 2904 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: 16.70 Time building geometry restraints manager: 14.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 28069 1.03 - 1.22: 35 1.22 - 1.42: 11145 1.42 - 1.61: 16731 1.61 - 1.81: 192 Bond restraints: 56172 Sorted by residual: bond pdb=" C3' ATPC1 900 " pdb=" C4' ATPC1 900 " ideal model delta sigma weight residual 1.526 1.281 0.245 1.10e-02 8.26e+03 4.95e+02 bond pdb=" C3' ATPB1 900 " pdb=" C4' ATPB1 900 " ideal model delta sigma weight residual 1.526 1.281 0.245 1.10e-02 8.26e+03 4.95e+02 bond pdb=" C1' ATPA1 900 " pdb=" C2' ATPA1 900 " ideal model delta sigma weight residual 1.531 1.266 0.265 1.20e-02 6.94e+03 4.88e+02 bond pdb=" C3' ATPA1 900 " pdb=" C4' ATPA1 900 " ideal model delta sigma weight residual 1.526 1.284 0.242 1.10e-02 8.26e+03 4.83e+02 bond pdb=" C1' ATPB1 900 " pdb=" C2' ATPB1 900 " ideal model delta sigma weight residual 1.531 1.268 0.263 1.20e-02 6.94e+03 4.79e+02 ... (remaining 56167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.11: 101837 5.11 - 10.23: 54 10.23 - 15.34: 16 15.34 - 20.46: 3 20.46 - 25.57: 4 Bond angle restraints: 101914 Sorted by residual: angle pdb=" PB ATPA1 900 " pdb=" O3B ATPA1 900 " pdb=" PG ATPA1 900 " ideal model delta sigma weight residual 139.87 120.81 19.06 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PB ATPC1 900 " pdb=" O3B ATPC1 900 " pdb=" PG ATPC1 900 " ideal model delta sigma weight residual 139.87 121.89 17.98 1.00e+00 1.00e+00 3.23e+02 angle pdb=" PB ATPB1 900 " pdb=" O3B ATPB1 900 " pdb=" PG ATPB1 900 " ideal model delta sigma weight residual 139.87 122.82 17.05 1.00e+00 1.00e+00 2.91e+02 angle pdb=" PA ATPA1 900 " pdb=" O3A ATPA1 900 " pdb=" PB ATPA1 900 " ideal model delta sigma weight residual 136.83 121.90 14.93 1.00e+00 1.00e+00 2.23e+02 angle pdb=" PA ATPC1 900 " pdb=" O3A ATPC1 900 " pdb=" PB ATPC1 900 " ideal model delta sigma weight residual 136.83 123.72 13.11 1.00e+00 1.00e+00 1.72e+02 ... (remaining 101909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 25614 35.95 - 71.89: 541 71.89 - 107.84: 16 107.84 - 143.78: 2 143.78 - 179.73: 1 Dihedral angle restraints: 26174 sinusoidal: 14760 harmonic: 11414 Sorted by residual: dihedral pdb=" CD ARGF1 375 " pdb=" NE ARGF1 375 " pdb=" CZ ARGF1 375 " pdb=" NH1 ARGF1 375 " ideal model delta sinusoidal sigma weight residual 0.00 -179.73 179.73 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA TYRF1 364 " pdb=" C TYRF1 364 " pdb=" N PROF1 365 " pdb=" CA PROF1 365 " ideal model delta harmonic sigma weight residual 180.00 131.01 48.99 0 5.00e+00 4.00e-02 9.60e+01 dihedral pdb=" CA ASPB1 300 " pdb=" C ASPB1 300 " pdb=" N ASPB1 301 " pdb=" CA ASPB1 301 " ideal model delta harmonic sigma weight residual -180.00 -135.06 -44.94 0 5.00e+00 4.00e-02 8.08e+01 ... (remaining 26171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3246 0.046 - 0.093: 984 0.093 - 0.139: 176 0.139 - 0.185: 8 0.185 - 0.231: 4 Chirality restraints: 4418 Sorted by residual: chirality pdb=" C2' ATPB1 900 " pdb=" C1' ATPB1 900 " pdb=" C3' ATPB1 900 " pdb=" O2' ATPB1 900 " both_signs ideal model delta sigma weight residual False -2.68 -2.45 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C2' ATPA1 900 " pdb=" C1' ATPA1 900 " pdb=" C3' ATPA1 900 " pdb=" O2' ATPA1 900 " both_signs ideal model delta sigma weight residual False -2.68 -2.46 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C3' ATPB1 900 " pdb=" C2' ATPB1 900 " pdb=" C4' ATPB1 900 " pdb=" O3' ATPB1 900 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 4415 not shown) Planarity restraints: 8360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASNB1 216 " 0.023 2.00e-02 2.50e+03 4.03e-02 2.43e+01 pdb=" CG ASNB1 216 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASNB1 216 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASNB1 216 " 0.070 2.00e-02 2.50e+03 pdb="HD21 ASNB1 216 " 0.002 2.00e-02 2.50e+03 pdb="HD22 ASNB1 216 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYRF1 364 " 0.056 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PROF1 365 " -0.148 5.00e-02 4.00e+02 pdb=" CA PROF1 365 " 0.045 5.00e-02 4.00e+02 pdb=" CD PROF1 365 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HISE1 386 " 0.012 2.00e-02 2.50e+03 1.30e-02 3.79e+00 pdb=" CG HISE1 386 " -0.030 2.00e-02 2.50e+03 pdb=" ND1 HISE1 386 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 HISE1 386 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 HISE1 386 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 HISE1 386 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 HISE1 386 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 HISE1 386 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 HISE1 386 " 0.007 2.00e-02 2.50e+03 ... (remaining 8357 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 1618 2.10 - 2.72: 101862 2.72 - 3.35: 163508 3.35 - 3.97: 208814 3.97 - 4.60: 336160 Nonbonded interactions: 811962 Sorted by model distance: nonbonded pdb="HH22 ARGE1 112 " pdb=" O GLYE1 125 " model vdw 1.473 2.450 nonbonded pdb=" OE1 GLNE1 301 " pdb=" H GLNE1 301 " model vdw 1.484 2.450 nonbonded pdb=" OE1 GLNF1 301 " pdb=" H GLNF1 301 " model vdw 1.487 2.450 nonbonded pdb=" OE1 GLND1 301 " pdb=" H GLND1 301 " model vdw 1.513 2.450 nonbonded pdb=" OE2 GLUF1 150 " pdb=" HE ARGF1 167 " model vdw 1.528 2.450 ... (remaining 811957 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A1' and (resid 34 through 205 or (resid 206 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 207 through 403 \ or (resid 404 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE \ or name HH11 or name HH12 or name HH22)) or resid 405 through 544 or resid 900 t \ hrough 1001)) selection = chain 'B1' selection = (chain 'C1' and ((resid 34 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 35 through 205 or (resid 206 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name CE or name NZ or name HA or name HB2 \ or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name \ HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 207 through 403 or (resid 40 \ 4 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or \ name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 \ or name HH12 or name HH22)) or resid 405 through 544 or resid 900 through 1001) \ ) } ncs_group { reference = (chain 'D1' and ((resid 28 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 29 through 374 or (re \ sid 375 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name H \ B2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or nam \ e HH21 or name HH22)) or resid 376 through 496)) selection = (chain 'E1' and ((resid 28 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 29 through 374 or (re \ sid 375 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name H \ B2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or nam \ e HH21 or name HH22)) or resid 376 through 496)) selection = (chain 'F1' and (resid 28 through 181 or (resid 182 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 183 through 496)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.950 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: 0.800 Extract box with map and model: 1.650 Check model and map are aligned: 0.340 Set scattering table: 0.400 Process input model: 90.910 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 : 0.009 0.292 28070 Z= 0.624 Angle : 0.755 25.572 37949 Z= 0.449 Chirality : 0.043 0.231 4418 Planarity : 0.003 0.085 4907 Dihedral : 9.972 179.730 10621 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.27 % Allowed : 5.04 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.09 % 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: -0.60 (0.14), residues: 3570 helix: 0.59 (0.12), residues: 1648 sheet: -0.84 (0.24), residues: 452 loop : -1.34 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP b 379 HIS 0.021 0.002 HISE1 386 PHE 0.021 0.002 PHED1 437 TYR 0.018 0.002 TYRB1 368 ARG 0.011 0.001 ARG b 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 536 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 528 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g1 46 MET cc_start: 0.8810 (mtm) cc_final: 0.8573 (mtp) REVERT: g1 259 MET cc_start: 0.8157 (mmp) cc_final: 0.7706 (mmp) REVERT: g1 268 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7485 (mt-10) REVERT: C1 380 GLN cc_start: 0.8150 (pm20) cc_final: 0.7912 (pp30) REVERT: C1 522 GLU cc_start: 0.7795 (tp30) cc_final: 0.7576 (tp30) REVERT: C1 534 LEU cc_start: 0.8715 (tt) cc_final: 0.8098 (tm) REVERT: i1 36 LYS cc_start: 0.8641 (mttm) cc_final: 0.8332 (mtmt) REVERT: b 229 GLU cc_start: 0.7757 (tp30) cc_final: 0.7473 (tp30) REVERT: d 87 ILE cc_start: 0.7556 (tp) cc_final: 0.7312 (pp) REVERT: d 97 LYS cc_start: 0.8938 (tttp) cc_final: 0.8440 (ttmm) outliers start: 8 outliers final: 1 residues processed: 531 average time/residue: 2.8802 time to fit residues: 1758.5997 Evaluate side-chains 256 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 255 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G1 residue 165 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 0.7980 chunk 269 optimal weight: 0.2980 chunk 149 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 279 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 169 optimal weight: 0.5980 chunk 207 optimal weight: 0.9980 chunk 323 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1 113 ASN G1 165 GLN C1 79 GLN C1 109 ASN C1 253 GLN C1 436 GLN C1 472 GLN C1 502 HIS C1 537 GLN B1 216 ASN ** B1 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1 404 GLN E1 452 ASN d 59 GLN d 74 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28070 Z= 0.208 Angle : 0.570 9.056 37949 Z= 0.297 Chirality : 0.041 0.181 4418 Planarity : 0.004 0.083 4907 Dihedral : 7.406 179.062 3982 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.11 % Allowed : 11.99 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.09 % 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: -0.00 (0.14), residues: 3570 helix: 1.09 (0.12), residues: 1651 sheet: -1.04 (0.24), residues: 442 loop : -0.86 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRPi1 33 HIS 0.016 0.001 HISE1 62 PHE 0.014 0.001 PHEA1 287 TYR 0.013 0.001 TYRB1 428 ARG 0.007 0.000 ARGA1 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 318 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 285 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G1 161 GLN cc_start: 0.8291 (tm130) cc_final: 0.7616 (tp40) REVERT: G1 165 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7824 (mm110) REVERT: g1 46 MET cc_start: 0.8972 (mtm) cc_final: 0.8720 (mtp) REVERT: C1 380 GLN cc_start: 0.8170 (pm20) cc_final: 0.7922 (pp30) REVERT: C1 384 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7590 (mm-30) REVERT: C1 522 GLU cc_start: 0.7995 (tp30) cc_final: 0.7782 (tm-30) REVERT: B1 522 GLU cc_start: 0.7852 (tp30) cc_final: 0.7547 (tp30) REVERT: B1 526 ASN cc_start: 0.8437 (m-40) cc_final: 0.7723 (m-40) REVERT: i1 36 LYS cc_start: 0.8548 (mttm) cc_final: 0.8272 (mtmt) REVERT: i1 47 ASP cc_start: 0.7916 (m-30) cc_final: 0.7716 (m-30) REVERT: s 136 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7923 (t) REVERT: b 37 ARG cc_start: 0.9066 (mmm160) cc_final: 0.8778 (mmp-170) REVERT: b 216 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8603 (tm-30) REVERT: b 361 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7852 (pmmt) outliers start: 33 outliers final: 8 residues processed: 307 average time/residue: 2.5275 time to fit residues: 915.7948 Evaluate side-chains 252 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 242 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G1 residue 213 GLU Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain C1 residue 538 GLU Chi-restraints excluded: chain D1 residue 485 SER Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain A1 residue 93 MET Chi-restraints excluded: chain A1 residue 435 SER Chi-restraints excluded: chain s residue 136 VAL Chi-restraints excluded: chain b residue 361 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 323 optimal weight: 9.9990 chunk 349 optimal weight: 4.9990 chunk 288 optimal weight: 0.7980 chunk 321 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 79 GLN B1 448 GLN ** B1 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1 404 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 28070 Z= 0.361 Angle : 0.590 11.737 37949 Z= 0.307 Chirality : 0.042 0.269 4418 Planarity : 0.005 0.185 4907 Dihedral : 7.717 179.018 3979 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.44 % Allowed : 11.95 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.09 % 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: 0.14 (0.14), residues: 3570 helix: 1.20 (0.13), residues: 1659 sheet: -1.06 (0.23), residues: 470 loop : -0.73 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRPi1 33 HIS 0.017 0.001 HISE1 62 PHE 0.020 0.001 PHED1 437 TYR 0.012 0.001 TYRD1 216 ARG 0.008 0.001 ARGF1 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 250 time to evaluate : 3.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G1 161 GLN cc_start: 0.8540 (tm130) cc_final: 0.7758 (tp40) REVERT: C1 380 GLN cc_start: 0.8365 (pm20) cc_final: 0.8044 (pm20) REVERT: C1 522 GLU cc_start: 0.8044 (tp30) cc_final: 0.7751 (tm-30) REVERT: D1 82 MET cc_start: 0.8693 (mmt) cc_final: 0.7799 (mmt) REVERT: B1 257 MET cc_start: 0.8730 (tpt) cc_final: 0.8480 (tpt) REVERT: F1 220 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7757 (mtm) REVERT: F1 449 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8144 (mmp-170) REVERT: A1 56 ILE cc_start: 0.9186 (pt) cc_final: 0.8869 (pp) REVERT: A1 435 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.8116 (p) REVERT: E1 82 MET cc_start: 0.8667 (mmp) cc_final: 0.7941 (mmt) REVERT: E1 439 MET cc_start: 0.8188 (mmm) cc_final: 0.7986 (mmp) REVERT: i1 36 LYS cc_start: 0.8620 (mttm) cc_final: 0.8338 (mtmt) REVERT: b 37 ARG cc_start: 0.9046 (mmm160) cc_final: 0.8760 (mmp-170) REVERT: b 361 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7996 (pmmt) REVERT: d 34 GLN cc_start: 0.8268 (mt0) cc_final: 0.8050 (mt0) REVERT: d 101 GLU cc_start: 0.8815 (mp0) cc_final: 0.8326 (mp0) outliers start: 43 outliers final: 16 residues processed: 282 average time/residue: 2.5737 time to fit residues: 863.4532 Evaluate side-chains 242 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 222 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 58 GLU Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain C1 residue 425 LEU Chi-restraints excluded: chain C1 residue 537 GLN Chi-restraints excluded: chain C1 residue 538 GLU Chi-restraints excluded: chain C1 residue 543 LEU Chi-restraints excluded: chain B1 residue 366 SER Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 220 MET Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain F1 residue 449 ARG Chi-restraints excluded: chain A1 residue 435 SER Chi-restraints excluded: chain A1 residue 508 SER Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain b residue 361 LYS Chi-restraints excluded: chain d residue 79 ASP Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 125 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 154 optimal weight: 0.5980 chunk 217 optimal weight: 4.9990 chunk 325 optimal weight: 3.9990 chunk 344 optimal weight: 6.9990 chunk 169 optimal weight: 0.6980 chunk 308 optimal weight: 0.0020 chunk 92 optimal weight: 2.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1 73 GLN C1 79 GLN C1 420 ASN C1 537 GLN B1 502 HIS A1 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28070 Z= 0.182 Angle : 0.525 11.875 37949 Z= 0.271 Chirality : 0.040 0.162 4418 Planarity : 0.004 0.082 4907 Dihedral : 7.375 179.900 3979 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.18 % Allowed : 13.20 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.06 % 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 (0.14), residues: 3570 helix: 1.42 (0.13), residues: 1658 sheet: -1.16 (0.24), residues: 434 loop : -0.64 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRPi1 33 HIS 0.014 0.001 HISE1 62 PHE 0.014 0.001 PHEA1 434 TYR 0.012 0.001 TYRB1 428 ARG 0.007 0.000 ARGB1 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 243 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g1 260 GLU cc_start: 0.8224 (tp30) cc_final: 0.7917 (tp30) REVERT: C1 109 ASN cc_start: 0.7752 (m-40) cc_final: 0.7511 (m110) REVERT: C1 380 GLN cc_start: 0.8344 (pm20) cc_final: 0.8038 (pm20) REVERT: C1 522 GLU cc_start: 0.8065 (tp30) cc_final: 0.7754 (tm-30) REVERT: D1 228 LYS cc_start: 0.8490 (tttm) cc_final: 0.7920 (tttm) REVERT: D1 231 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7100 (mt-10) REVERT: B1 257 MET cc_start: 0.8723 (tpt) cc_final: 0.8503 (tpt) REVERT: B1 360 THR cc_start: 0.8431 (m) cc_final: 0.8177 (p) REVERT: B1 522 GLU cc_start: 0.7876 (tp30) cc_final: 0.7580 (tp30) REVERT: B1 526 ASN cc_start: 0.8412 (m-40) cc_final: 0.7878 (m-40) REVERT: F1 220 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7705 (mtm) REVERT: F1 404 GLN cc_start: 0.8279 (mt0) cc_final: 0.7963 (mt0) REVERT: A1 56 ILE cc_start: 0.9184 (pt) cc_final: 0.8871 (pp) REVERT: A1 435 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8078 (p) REVERT: E1 82 MET cc_start: 0.8706 (mmp) cc_final: 0.8103 (mmt) REVERT: E1 410 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7555 (pp) REVERT: E1 465 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: i1 36 LYS cc_start: 0.8595 (mttm) cc_final: 0.8336 (mtmt) REVERT: b 37 ARG cc_start: 0.9070 (mmm160) cc_final: 0.8795 (mmp-170) REVERT: d 101 GLU cc_start: 0.8767 (mp0) cc_final: 0.8290 (mp0) outliers start: 35 outliers final: 14 residues processed: 268 average time/residue: 2.3888 time to fit residues: 759.3844 Evaluate side-chains 243 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 225 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 58 GLU Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain C1 residue 425 LEU Chi-restraints excluded: chain C1 residue 537 GLN Chi-restraints excluded: chain C1 residue 538 GLU Chi-restraints excluded: chain C1 residue 543 LEU Chi-restraints excluded: chain F1 residue 220 MET Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain A1 residue 417 ILE Chi-restraints excluded: chain A1 residue 435 SER Chi-restraints excluded: chain A1 residue 508 SER Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain E1 residue 376 MET Chi-restraints excluded: chain E1 residue 410 LEU Chi-restraints excluded: chain E1 residue 465 GLU Chi-restraints excluded: chain d residue 87 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 293 optimal weight: 0.0770 chunk 237 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 308 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 79 GLN C1 537 GLN E1 404 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 28070 Z= 0.325 Angle : 0.550 10.772 37949 Z= 0.288 Chirality : 0.041 0.155 4418 Planarity : 0.004 0.082 4907 Dihedral : 7.346 179.512 3979 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.14 % Allowed : 13.33 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.06 % 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 (0.14), residues: 3570 helix: 1.41 (0.13), residues: 1656 sheet: -1.18 (0.24), residues: 450 loop : -0.63 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 83 HIS 0.015 0.001 HISE1 62 PHE 0.016 0.001 PHED1 437 TYR 0.013 0.001 TYR d 108 ARG 0.006 0.000 ARGE1 490 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 234 time to evaluate : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g1 260 GLU cc_start: 0.8269 (tp30) cc_final: 0.7992 (tp30) REVERT: C1 380 GLN cc_start: 0.8431 (pm20) cc_final: 0.8042 (pm20) REVERT: C1 522 GLU cc_start: 0.8167 (tp30) cc_final: 0.7810 (tm-30) REVERT: B1 522 GLU cc_start: 0.7965 (tp30) cc_final: 0.7630 (tp30) REVERT: B1 526 ASN cc_start: 0.8532 (m-40) cc_final: 0.7831 (m-40) REVERT: F1 449 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.7973 (mmp-170) REVERT: A1 56 ILE cc_start: 0.9234 (pt) cc_final: 0.8908 (pp) REVERT: A1 435 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.8051 (p) REVERT: E1 82 MET cc_start: 0.8817 (mmp) cc_final: 0.8179 (mmt) REVERT: E1 410 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7513 (pp) REVERT: i1 36 LYS cc_start: 0.8647 (mttm) cc_final: 0.8397 (mtmt) REVERT: b 37 ARG cc_start: 0.9065 (mmm160) cc_final: 0.8785 (mmp-170) REVERT: d 101 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8283 (mp0) outliers start: 34 outliers final: 16 residues processed: 254 average time/residue: 2.4926 time to fit residues: 751.4200 Evaluate side-chains 237 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 217 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain C1 residue 425 LEU Chi-restraints excluded: chain C1 residue 538 GLU Chi-restraints excluded: chain C1 residue 543 LEU Chi-restraints excluded: chain D1 residue 378 ASP Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain F1 residue 449 ARG Chi-restraints excluded: chain A1 residue 93 MET Chi-restraints excluded: chain A1 residue 417 ILE Chi-restraints excluded: chain A1 residue 435 SER Chi-restraints excluded: chain A1 residue 508 SER Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain E1 residue 410 LEU Chi-restraints excluded: chain E1 residue 465 GLU Chi-restraints excluded: chain b residue 212 THR Chi-restraints excluded: chain b residue 361 LYS Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 101 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 202 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 344 optimal weight: 6.9990 chunk 285 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1 181 GLN C1 420 ASN ** F1 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28070 Z= 0.230 Angle : 0.520 6.631 37949 Z= 0.269 Chirality : 0.040 0.160 4418 Planarity : 0.003 0.081 4907 Dihedral : 6.957 179.561 3979 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.24 % Allowed : 13.36 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.03 % 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: 0.47 (0.14), residues: 3570 helix: 1.55 (0.13), residues: 1661 sheet: -1.19 (0.25), residues: 424 loop : -0.60 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 83 HIS 0.013 0.001 HISE1 62 PHE 0.013 0.001 PHED1 437 TYR 0.019 0.001 TYRB1 428 ARG 0.005 0.000 ARGE1 490 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 238 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g1 260 GLU cc_start: 0.8249 (tp30) cc_final: 0.7991 (tp30) REVERT: C1 522 GLU cc_start: 0.8200 (tp30) cc_final: 0.7852 (tm-30) REVERT: B1 522 GLU cc_start: 0.7956 (tp30) cc_final: 0.7588 (tp30) REVERT: B1 526 ASN cc_start: 0.8540 (m-40) cc_final: 0.7768 (m-40) REVERT: A1 56 ILE cc_start: 0.9247 (pt) cc_final: 0.8938 (pp) REVERT: E1 82 MET cc_start: 0.8852 (mmp) cc_final: 0.8136 (mmt) REVERT: E1 410 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7535 (pp) REVERT: i1 36 LYS cc_start: 0.8652 (mttm) cc_final: 0.8407 (mtmt) REVERT: b 37 ARG cc_start: 0.9069 (mmm160) cc_final: 0.8745 (mmp-170) REVERT: d 101 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8270 (mp0) outliers start: 37 outliers final: 16 residues processed: 262 average time/residue: 2.4566 time to fit residues: 759.8269 Evaluate side-chains 242 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 224 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain C1 residue 425 LEU Chi-restraints excluded: chain C1 residue 538 GLU Chi-restraints excluded: chain C1 residue 543 LEU Chi-restraints excluded: chain D1 residue 378 ASP Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain A1 residue 93 MET Chi-restraints excluded: chain A1 residue 417 ILE Chi-restraints excluded: chain A1 residue 508 SER Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain E1 residue 410 LEU Chi-restraints excluded: chain E1 residue 465 GLU Chi-restraints excluded: chain b residue 212 THR Chi-restraints excluded: chain b residue 361 LYS Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 101 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 343 optimal weight: 8.9990 chunk 214 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 420 ASN C1 537 GLN E1 404 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28070 Z= 0.269 Angle : 0.529 8.002 37949 Z= 0.275 Chirality : 0.040 0.157 4418 Planarity : 0.003 0.080 4907 Dihedral : 6.935 178.800 3979 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.04 % Allowed : 13.90 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3570 helix: 1.57 (0.13), residues: 1661 sheet: -1.19 (0.25), residues: 419 loop : -0.57 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 83 HIS 0.011 0.001 HISE1 62 PHE 0.014 0.001 PHED1 437 TYR 0.016 0.001 TYRB1 428 ARG 0.005 0.000 ARGE1 490 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 233 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G1 161 GLN cc_start: 0.8431 (tm130) cc_final: 0.8076 (tp40) REVERT: g1 260 GLU cc_start: 0.8271 (tp30) cc_final: 0.8060 (tp30) REVERT: C1 522 GLU cc_start: 0.8258 (tp30) cc_final: 0.7908 (tm-30) REVERT: B1 516 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8613 (m-30) REVERT: B1 522 GLU cc_start: 0.8019 (tp30) cc_final: 0.7661 (tp30) REVERT: B1 526 ASN cc_start: 0.8554 (m-40) cc_final: 0.7765 (m-40) REVERT: A1 56 ILE cc_start: 0.9257 (pt) cc_final: 0.8947 (pp) REVERT: E1 82 MET cc_start: 0.8895 (mmp) cc_final: 0.8180 (mmt) REVERT: E1 376 MET cc_start: 0.8616 (mmm) cc_final: 0.8394 (mmm) REVERT: E1 410 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7495 (pp) REVERT: i1 36 LYS cc_start: 0.8654 (mttm) cc_final: 0.8413 (mtmt) REVERT: b 37 ARG cc_start: 0.9090 (mmm160) cc_final: 0.8754 (mmp-170) REVERT: d 101 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: d 111 ASP cc_start: 0.8613 (p0) cc_final: 0.8181 (m-30) outliers start: 31 outliers final: 19 residues processed: 253 average time/residue: 2.4449 time to fit residues: 735.1538 Evaluate side-chains 248 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 226 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain C1 residue 420 ASN Chi-restraints excluded: chain C1 residue 425 LEU Chi-restraints excluded: chain C1 residue 537 GLN Chi-restraints excluded: chain C1 residue 538 GLU Chi-restraints excluded: chain C1 residue 543 LEU Chi-restraints excluded: chain D1 residue 378 ASP Chi-restraints excluded: chain B1 residue 516 ASP Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain A1 residue 93 MET Chi-restraints excluded: chain A1 residue 300 ASP Chi-restraints excluded: chain A1 residue 417 ILE Chi-restraints excluded: chain A1 residue 508 SER Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain E1 residue 410 LEU Chi-restraints excluded: chain E1 residue 465 GLU Chi-restraints excluded: chain b residue 212 THR Chi-restraints excluded: chain b residue 361 LYS Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 101 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 0.9990 chunk 137 optimal weight: 0.0060 chunk 204 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1 181 GLN C1 537 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28070 Z= 0.218 Angle : 0.524 9.083 37949 Z= 0.271 Chirality : 0.040 0.159 4418 Planarity : 0.003 0.080 4907 Dihedral : 6.859 178.731 3979 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.94 % Allowed : 14.24 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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 (0.14), residues: 3570 helix: 1.61 (0.13), residues: 1660 sheet: -1.15 (0.26), residues: 419 loop : -0.53 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 83 HIS 0.010 0.001 HISE1 62 PHE 0.012 0.001 PHEi1 46 TYR 0.026 0.001 TYRB1 428 ARG 0.008 0.000 ARGB1 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 238 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G1 161 GLN cc_start: 0.8482 (tm130) cc_final: 0.8126 (tp40) REVERT: C1 522 GLU cc_start: 0.8262 (tp30) cc_final: 0.7905 (tm-30) REVERT: B1 360 THR cc_start: 0.8525 (m) cc_final: 0.8272 (p) REVERT: B1 516 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8597 (m-30) REVERT: F1 233 ARG cc_start: 0.7989 (mpt-90) cc_final: 0.7700 (mpp80) REVERT: F1 404 GLN cc_start: 0.8146 (mt0) cc_final: 0.7781 (mt0) REVERT: A1 56 ILE cc_start: 0.9255 (pt) cc_final: 0.8949 (pp) REVERT: E1 82 MET cc_start: 0.8866 (mmp) cc_final: 0.8191 (mmt) REVERT: E1 376 MET cc_start: 0.8624 (mmm) cc_final: 0.8387 (mmm) REVERT: E1 410 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7499 (pp) REVERT: i1 36 LYS cc_start: 0.8658 (mttm) cc_final: 0.8425 (mtmt) REVERT: b 37 ARG cc_start: 0.9086 (mmm160) cc_final: 0.8750 (mmp-170) REVERT: d 101 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8300 (mp0) REVERT: d 111 ASP cc_start: 0.8612 (p0) cc_final: 0.8339 (m-30) outliers start: 28 outliers final: 16 residues processed: 257 average time/residue: 2.4548 time to fit residues: 758.2293 Evaluate side-chains 243 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 224 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain C1 residue 425 LEU Chi-restraints excluded: chain C1 residue 538 GLU Chi-restraints excluded: chain C1 residue 543 LEU Chi-restraints excluded: chain B1 residue 516 ASP Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain A1 residue 93 MET Chi-restraints excluded: chain A1 residue 300 ASP Chi-restraints excluded: chain A1 residue 417 ILE Chi-restraints excluded: chain A1 residue 508 SER Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain E1 residue 410 LEU Chi-restraints excluded: chain E1 residue 465 GLU Chi-restraints excluded: chain b residue 212 THR Chi-restraints excluded: chain b residue 361 LYS Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 101 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 0.7980 chunk 328 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 319 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 chunk 302 optimal weight: 0.8980 chunk 318 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1 73 GLN C1 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28070 Z= 0.232 Angle : 0.531 10.012 37949 Z= 0.274 Chirality : 0.040 0.158 4418 Planarity : 0.003 0.080 4907 Dihedral : 6.838 178.637 3979 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.87 % Allowed : 14.34 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: 0.58 (0.14), residues: 3570 helix: 1.62 (0.13), residues: 1661 sheet: -1.13 (0.26), residues: 419 loop : -0.51 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 83 HIS 0.009 0.001 HISE1 62 PHE 0.013 0.001 PHED1 437 TYR 0.020 0.001 TYRB1 428 ARG 0.007 0.000 ARGE1 490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 228 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G1 161 GLN cc_start: 0.8484 (tm130) cc_final: 0.8118 (tp40) REVERT: B1 516 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8613 (m-30) REVERT: F1 233 ARG cc_start: 0.8018 (mpt-90) cc_final: 0.7713 (mpp80) REVERT: A1 56 ILE cc_start: 0.9256 (pt) cc_final: 0.8952 (pp) REVERT: E1 82 MET cc_start: 0.8911 (mmp) cc_final: 0.8257 (mmt) REVERT: E1 376 MET cc_start: 0.8605 (mmm) cc_final: 0.8386 (mmm) REVERT: E1 410 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7485 (pp) REVERT: E1 490 ARG cc_start: 0.8393 (ttp-110) cc_final: 0.8175 (ttm-80) REVERT: i1 36 LYS cc_start: 0.8682 (mttm) cc_final: 0.8462 (mtmt) REVERT: b 37 ARG cc_start: 0.9112 (mmm160) cc_final: 0.8751 (mmp-170) REVERT: d 101 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8306 (mp0) outliers start: 26 outliers final: 16 residues processed: 247 average time/residue: 2.4034 time to fit residues: 705.2845 Evaluate side-chains 245 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 226 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain C1 residue 425 LEU Chi-restraints excluded: chain C1 residue 538 GLU Chi-restraints excluded: chain C1 residue 543 LEU Chi-restraints excluded: chain B1 residue 516 ASP Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain A1 residue 300 ASP Chi-restraints excluded: chain A1 residue 417 ILE Chi-restraints excluded: chain A1 residue 508 SER Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain E1 residue 410 LEU Chi-restraints excluded: chain E1 residue 465 GLU Chi-restraints excluded: chain s residue 145 ILE Chi-restraints excluded: chain b residue 212 THR Chi-restraints excluded: chain b residue 361 LYS Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 1.9990 chunk 338 optimal weight: 6.9990 chunk 206 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 235 optimal weight: 0.0020 chunk 354 optimal weight: 0.9990 chunk 326 optimal weight: 9.9990 chunk 282 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 218 optimal weight: 0.7980 chunk 173 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28070 Z= 0.166 Angle : 0.521 11.252 37949 Z= 0.267 Chirality : 0.040 0.158 4418 Planarity : 0.003 0.079 4907 Dihedral : 6.641 178.599 3979 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.57 % Allowed : 14.98 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: 0.70 (0.15), residues: 3570 helix: 1.73 (0.13), residues: 1660 sheet: -1.08 (0.26), residues: 419 loop : -0.45 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 83 HIS 0.008 0.001 HISE1 62 PHE 0.011 0.001 PHEi1 46 TYR 0.022 0.001 TYRB1 428 ARG 0.009 0.000 ARGB1 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 241 time to evaluate : 3.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 534 LEU cc_start: 0.8720 (tm) cc_final: 0.8282 (tm) REVERT: B1 360 THR cc_start: 0.8486 (m) cc_final: 0.8243 (p) REVERT: B1 516 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8579 (m-30) REVERT: B1 522 GLU cc_start: 0.7905 (tp30) cc_final: 0.7590 (tp30) REVERT: B1 526 ASN cc_start: 0.8422 (m-40) cc_final: 0.7945 (m-40) REVERT: F1 404 GLN cc_start: 0.8164 (mt0) cc_final: 0.7904 (mt0) REVERT: A1 56 ILE cc_start: 0.9248 (pt) cc_final: 0.8947 (pp) REVERT: E1 82 MET cc_start: 0.8891 (mmp) cc_final: 0.8253 (mmt) REVERT: E1 376 MET cc_start: 0.8609 (mmm) cc_final: 0.8402 (mmm) REVERT: E1 410 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7481 (pp) REVERT: E1 490 ARG cc_start: 0.8390 (ttp-110) cc_final: 0.8183 (ttm-80) REVERT: i1 36 LYS cc_start: 0.8669 (mttm) cc_final: 0.8461 (mtmt) REVERT: b 37 ARG cc_start: 0.9091 (mmm160) cc_final: 0.8758 (mmp-170) REVERT: d 101 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: d 115 LYS cc_start: 0.8825 (mmpt) cc_final: 0.8453 (mmtm) outliers start: 17 outliers final: 10 residues processed: 250 average time/residue: 2.4361 time to fit residues: 730.9407 Evaluate side-chains 241 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 228 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 384 GLU Chi-restraints excluded: chain C1 residue 543 LEU Chi-restraints excluded: chain D1 residue 376 MET Chi-restraints excluded: chain B1 residue 516 ASP Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain A1 residue 417 ILE Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain E1 residue 410 LEU Chi-restraints excluded: chain E1 residue 465 GLU Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 282 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 290 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.083022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.060962 restraints weight = 182664.230| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.38 r_work: 0.2833 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28070 Z= 0.211 Angle : 0.529 11.400 37949 Z= 0.272 Chirality : 0.040 0.154 4418 Planarity : 0.003 0.079 4907 Dihedral : 6.607 178.664 3979 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.60 % Allowed : 15.11 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: 0.69 (0.14), residues: 3570 helix: 1.72 (0.13), residues: 1660 sheet: -1.09 (0.26), residues: 419 loop : -0.45 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 83 HIS 0.005 0.001 HISE1 386 PHE 0.011 0.001 PHEi1 46 TYR 0.021 0.001 TYRB1 428 ARG 0.006 0.000 ARGE1 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15469.05 seconds wall clock time: 264 minutes 35.83 seconds (15875.83 seconds total)