Starting phenix.real_space_refine on Wed Apr 10 03:55:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtl_14144/04_2024/7qtl_14144_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtl_14144/04_2024/7qtl_14144.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtl_14144/04_2024/7qtl_14144_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtl_14144/04_2024/7qtl_14144_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtl_14144/04_2024/7qtl_14144_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtl_14144/04_2024/7qtl_14144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtl_14144/04_2024/7qtl_14144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtl_14144/04_2024/7qtl_14144_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtl_14144/04_2024/7qtl_14144_updated.pdb" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 2 5.21 5 S 126 5.16 5 C 11329 2.51 5 N 3199 2.21 5 O 3691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B GLU 614": "OE1" <-> "OE2" Residue "C GLU 361": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 18397 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5755 Classifications: {'peptide': 709} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 676} Chain breaks: 1 Chain: "B" Number of atoms: 5736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 717, 5728 Classifications: {'peptide': 717} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 686} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 717, 5728 Classifications: {'peptide': 717} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 686} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 5829 Chain: "C" Number of atoms: 5767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5767 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 29, 'TRANS': 696} Chain breaks: 2 Chain: "V" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 284 Classifications: {'RNA': 13} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "R" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "M" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 365 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, '2TM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'GTA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "V" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALEU B 218 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU B 218 " occ=0.50 Time building chain proxies: 12.79, per 1000 atoms: 0.70 Number of scatterers: 18397 At special positions: 0 Unit cell: (117.029, 126.781, 122.718, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 126 16.00 P 50 15.00 Mg 2 11.99 O 3691 8.00 N 3199 7.00 C 11329 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.27 Conformation dependent library (CDL) restraints added in 4.9 seconds 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4054 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 22 sheets defined 43.7% alpha, 11.9% beta 10 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 11.49 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 11 through 23 Processing helix chain 'A' and resid 32 through 49 Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 165 through 184 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 381 through 384 No H-bonds generated for 'chain 'A' and resid 381 through 384' Processing helix chain 'A' and resid 406 through 414 Processing helix chain 'A' and resid 434 through 451 Processing helix chain 'A' and resid 454 through 475 Processing helix chain 'A' and resid 534 through 537 Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 581 through 603 removed outlier: 4.085A pdb=" N GLN A 590 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 593 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A 601 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 633 through 649 Processing helix chain 'A' and resid 653 through 673 removed outlier: 4.173A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 4.061A pdb=" N CYS A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 715 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 15 through 21 removed outlier: 5.877A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 139 through 152 Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.996A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 246 through 265 removed outlier: 4.168A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 315 through 325 Processing helix chain 'B' and resid 331 through 345 removed outlier: 4.868A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 383 through 395 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.038A pdb=" N GLY B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 456 through 473 removed outlier: 3.536A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 519 through 536 Processing helix chain 'B' and resid 541 through 559 Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 586 through 588 No H-bonds generated for 'chain 'B' and resid 586 through 588' Processing helix chain 'B' and resid 591 through 593 No H-bonds generated for 'chain 'B' and resid 591 through 593' Processing helix chain 'B' and resid 601 through 603 No H-bonds generated for 'chain 'B' and resid 601 through 603' Processing helix chain 'B' and resid 608 through 611 No H-bonds generated for 'chain 'B' and resid 608 through 611' Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 682 through 699 Processing helix chain 'B' and resid 714 through 732 Processing helix chain 'B' and resid 737 through 755 Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 15 through 21 Processing helix chain 'C' and resid 25 through 33 removed outlier: 3.998A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 111 through 114 No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 116 through 126 Processing helix chain 'C' and resid 156 through 167 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 180 through 192 Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 226 through 229 No H-bonds generated for 'chain 'C' and resid 226 through 229' Processing helix chain 'C' and resid 232 through 235 No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 252 through 272 removed outlier: 4.118A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 285 Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 391 through 405 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 430 through 440 removed outlier: 3.639A pdb=" N LYS C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 449 Processing helix chain 'C' and resid 515 through 517 No H-bonds generated for 'chain 'C' and resid 515 through 517' Processing helix chain 'C' and resid 542 through 555 Processing helix chain 'C' and resid 557 through 566 removed outlier: 3.819A pdb=" N SER C 565 " --> pdb=" O LYS C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 572 Processing helix chain 'C' and resid 575 through 581 Proline residue: C 579 - end of helix Processing helix chain 'C' and resid 586 through 604 removed outlier: 4.576A pdb=" N GLY C 590 " --> pdb=" O LYS C 586 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLN C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 618 Processing helix chain 'C' and resid 620 through 622 No H-bonds generated for 'chain 'C' and resid 620 through 622' Processing helix chain 'C' and resid 702 through 704 No H-bonds generated for 'chain 'C' and resid 702 through 704' Processing helix chain 'C' and resid 710 through 712 No H-bonds generated for 'chain 'C' and resid 710 through 712' Processing sheet with id= A, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.137A pdb=" N HIS A 144 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY A 121 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N HIS A 146 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR A 123 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE A 148 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 290 through 292 removed outlier: 6.645A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 502 through 506 removed outlier: 3.649A pdb=" N VAL A 557 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 550 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU A 544 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 619 through 624 removed outlier: 6.792A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= F, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= G, first strand: chain 'B' and resid 178 through 182 Processing sheet with id= H, first strand: chain 'B' and resid 224 through 228 Processing sheet with id= I, first strand: chain 'B' and resid 483 through 486 Processing sheet with id= J, first strand: chain 'B' and resid 348 through 350 Processing sheet with id= K, first strand: chain 'B' and resid 355 through 359 Processing sheet with id= L, first strand: chain 'B' and resid 489 through 492 Processing sheet with id= M, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= N, first strand: chain 'C' and resid 133 through 135 Processing sheet with id= O, first strand: chain 'C' and resid 287 through 289 Processing sheet with id= P, first strand: chain 'C' and resid 323 through 325 removed outlier: 6.817A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA C 377 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 338 through 345 Processing sheet with id= R, first strand: chain 'C' and resid 451 through 453 Processing sheet with id= S, first strand: chain 'C' and resid 635 through 640 Processing sheet with id= T, first strand: chain 'C' and resid 720 through 724 removed outlier: 3.997A pdb=" N GLU C 720 " --> pdb=" O LYS C 736 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 698 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET C 735 " --> pdb=" O ILE C 696 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE C 696 " --> pdb=" O MET C 735 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.724A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 664 through 667 removed outlier: 3.781A pdb=" N GLY C 673 " --> pdb=" O LEU C 665 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL C 667 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASP C 671 " --> pdb=" O VAL C 667 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 1975 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 8.14 Time building geometry restraints manager: 8.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5716 1.34 - 1.46: 3420 1.46 - 1.58: 9266 1.58 - 1.70: 94 1.70 - 1.82: 222 Bond restraints: 18718 Sorted by residual: bond pdb=" C3B GTA M 101 " pdb=" C4B GTA M 101 " ideal model delta sigma weight residual 1.275 1.516 -0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C1B GTA M 101 " pdb=" C2B GTA M 101 " ideal model delta sigma weight residual 1.277 1.502 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1' 2TM B 901 " pdb=" C2' 2TM B 901 " ideal model delta sigma weight residual 1.327 1.534 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C5 GTA M 101 " pdb=" C6 GTA M 101 " ideal model delta sigma weight residual 1.541 1.336 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C1' 2TM B 901 " pdb=" O4' 2TM B 901 " ideal model delta sigma weight residual 1.609 1.412 0.197 2.00e-02 2.50e+03 9.71e+01 ... (remaining 18713 not shown) Histogram of bond angle deviations from ideal: 96.23 - 103.79: 399 103.79 - 111.36: 7974 111.36 - 118.93: 7282 118.93 - 126.50: 9423 126.50 - 134.07: 385 Bond angle restraints: 25463 Sorted by residual: angle pdb=" C5C GTA M 101 " pdb=" C6C GTA M 101 " pdb=" N6C GTA M 101 " ideal model delta sigma weight residual 130.29 116.20 14.09 3.00e+00 1.11e-01 2.20e+01 angle pdb=" N1C GTA M 101 " pdb=" C6C GTA M 101 " pdb=" N6C GTA M 101 " ideal model delta sigma weight residual 109.68 121.77 -12.09 3.00e+00 1.11e-01 1.62e+01 angle pdb=" N PRO A 28 " pdb=" CD PRO A 28 " pdb=" CG PRO A 28 " ideal model delta sigma weight residual 103.20 97.43 5.77 1.50e+00 4.44e-01 1.48e+01 angle pdb=" CA GLU A 243 " pdb=" CB GLU A 243 " pdb=" CG GLU A 243 " ideal model delta sigma weight residual 114.10 121.74 -7.64 2.00e+00 2.50e-01 1.46e+01 angle pdb=" C1A GTA M 101 " pdb=" N9 GTA M 101 " pdb=" C4 GTA M 101 " ideal model delta sigma weight residual 114.98 126.15 -11.17 3.00e+00 1.11e-01 1.39e+01 ... (remaining 25458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 10968 35.83 - 71.66: 458 71.66 - 107.49: 44 107.49 - 143.32: 1 143.32 - 179.15: 2 Dihedral angle restraints: 11473 sinusoidal: 5215 harmonic: 6258 Sorted by residual: dihedral pdb=" CD ARG B 287 " pdb=" NE ARG B 287 " pdb=" CZ ARG B 287 " pdb=" NH1 ARG B 287 " ideal model delta sinusoidal sigma weight residual 0.00 60.23 -60.23 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CA VAL C 220 " pdb=" C VAL C 220 " pdb=" N ALA C 221 " pdb=" CA ALA C 221 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLU A 352 " pdb=" C GLU A 352 " pdb=" N LYS A 353 " pdb=" CA LYS A 353 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 11470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2650 0.081 - 0.162: 182 0.162 - 0.242: 3 0.242 - 0.323: 4 0.323 - 0.404: 2 Chirality restraints: 2841 Sorted by residual: chirality pdb=" C2' 2TM B 901 " pdb=" C1' 2TM B 901 " pdb=" C3' 2TM B 901 " pdb=" O2' 2TM B 901 " both_signs ideal model delta sigma weight residual False -2.35 -2.75 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C3A GTA M 101 " pdb=" C2A GTA M 101 " pdb=" C4A GTA M 101 " pdb=" O3A GTA M 101 " both_signs ideal model delta sigma weight residual False -2.48 -2.82 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C4B GTA M 101 " pdb=" C3B GTA M 101 " pdb=" C5B GTA M 101 " pdb=" O4B GTA M 101 " both_signs ideal model delta sigma weight residual False -2.46 -2.77 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 2838 not shown) Planarity restraints: 3108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 287 " 0.753 9.50e-02 1.11e+02 3.39e-01 8.54e+01 pdb=" NE ARG B 287 " -0.070 2.00e-02 2.50e+03 pdb=" CZ ARG B 287 " 0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG B 287 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG B 287 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 582 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.58e+00 pdb=" C ARG A 582 " -0.054 2.00e-02 2.50e+03 pdb=" O ARG A 582 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 583 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 653 " -0.048 5.00e-02 4.00e+02 7.24e-02 8.40e+00 pdb=" N PRO C 654 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 654 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 654 " -0.040 5.00e-02 4.00e+02 ... (remaining 3105 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 198 2.57 - 3.15: 14505 3.15 - 3.74: 30583 3.74 - 4.32: 44883 4.32 - 4.90: 70216 Nonbonded interactions: 160385 Sorted by model distance: nonbonded pdb="MG MG B 902 " pdb=" O HOH B1015 " model vdw 1.988 2.170 nonbonded pdb="MG MG B 903 " pdb=" O HOH B1025 " model vdw 2.033 2.170 nonbonded pdb=" OD1 ASN C 301 " pdb=" OG1 THR C 303 " model vdw 2.120 2.440 nonbonded pdb=" OD2 ASP B 41 " pdb=" NH1 ARG B 45 " model vdw 2.131 2.520 nonbonded pdb=" OE1 GLU A 524 " pdb=" O HOH A 801 " model vdw 2.140 2.440 ... (remaining 160380 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 13.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 15.740 Check model and map are aligned: 0.270 Set scattering table: 0.200 Process input model: 65.620 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.241 18718 Z= 0.411 Angle : 0.660 14.085 25463 Z= 0.330 Chirality : 0.044 0.404 2841 Planarity : 0.008 0.339 3108 Dihedral : 18.134 179.147 7419 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.56 % Rotamer: Outliers : 3.98 % Allowed : 19.70 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.16), residues: 2137 helix: -0.37 (0.15), residues: 984 sheet: -1.02 (0.33), residues: 222 loop : -1.65 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 368 HIS 0.004 0.001 HIS B 562 PHE 0.015 0.001 PHE B 551 TYR 0.015 0.002 TYR A 48 ARG 0.069 0.001 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 241 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 411 MET cc_start: 0.8619 (mmp) cc_final: 0.8137 (mmp) REVERT: C 171 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7634 (mm-30) outliers start: 76 outliers final: 20 residues processed: 303 average time/residue: 1.8453 time to fit residues: 610.8242 Evaluate side-chains 180 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 556 GLN B 115 GLN B 310 ASN B 562 HIS ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 ASN C 75 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18718 Z= 0.348 Angle : 0.588 8.662 25463 Z= 0.307 Chirality : 0.043 0.188 2841 Planarity : 0.004 0.052 3108 Dihedral : 12.793 176.364 3061 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.14 % Allowed : 19.49 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2137 helix: 0.64 (0.16), residues: 979 sheet: -0.71 (0.32), residues: 240 loop : -1.09 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 422 HIS 0.004 0.001 HIS C 285 PHE 0.017 0.002 PHE A 4 TYR 0.019 0.002 TYR A 48 ARG 0.005 0.001 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 168 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 636 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6831 (tp30) REVERT: C 703 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7573 (ptm160) outliers start: 79 outliers final: 36 residues processed: 229 average time/residue: 1.6626 time to fit residues: 420.4040 Evaluate side-chains 188 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 510 ASN Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 703 ARG Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 715 ASN Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 163 optimal weight: 0.5980 chunk 133 optimal weight: 0.1980 chunk 54 optimal weight: 0.6980 chunk 196 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 157 optimal weight: 0.0470 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS A 346 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN B 532 ASN B 567 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18718 Z= 0.139 Angle : 0.481 6.705 25463 Z= 0.253 Chirality : 0.038 0.162 2841 Planarity : 0.004 0.042 3108 Dihedral : 12.435 175.751 3048 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.10 % Allowed : 21.27 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2137 helix: 1.20 (0.16), residues: 985 sheet: -0.36 (0.32), residues: 254 loop : -0.89 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 368 HIS 0.003 0.000 HIS A 128 PHE 0.014 0.001 PHE A 4 TYR 0.012 0.001 TYR B 497 ARG 0.005 0.000 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 166 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8103 (mm) REVERT: C 11 MET cc_start: 0.8903 (mmm) cc_final: 0.8611 (mmt) REVERT: C 294 MET cc_start: 0.8554 (ttt) cc_final: 0.8066 (ttt) REVERT: C 731 VAL cc_start: 0.8873 (t) cc_final: 0.8647 (t) outliers start: 40 outliers final: 16 residues processed: 197 average time/residue: 1.8272 time to fit residues: 394.3814 Evaluate side-chains 168 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 569 GLN Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 93 optimal weight: 0.5980 chunk 131 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 186 optimal weight: 0.0010 chunk 56 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18718 Z= 0.156 Angle : 0.479 9.935 25463 Z= 0.249 Chirality : 0.038 0.158 2841 Planarity : 0.003 0.042 3108 Dihedral : 12.225 175.992 3034 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.89 % Allowed : 21.22 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2137 helix: 1.44 (0.17), residues: 982 sheet: -0.24 (0.32), residues: 254 loop : -0.77 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 49 HIS 0.003 0.000 HIS B 184 PHE 0.016 0.001 PHE C 694 TYR 0.017 0.001 TYR A 48 ARG 0.007 0.000 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 156 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 493 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7172 (mtt180) outliers start: 36 outliers final: 20 residues processed: 184 average time/residue: 1.7235 time to fit residues: 350.3599 Evaluate side-chains 169 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 493 ARG Chi-restraints excluded: chain C residue 510 ASN Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 155 optimal weight: 0.0970 chunk 86 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 106 optimal weight: 0.0270 chunk 187 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN B 567 GLN C 715 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18718 Z= 0.193 Angle : 0.484 7.751 25463 Z= 0.252 Chirality : 0.039 0.158 2841 Planarity : 0.003 0.041 3108 Dihedral : 12.194 175.590 3033 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.41 % Allowed : 21.16 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2137 helix: 1.45 (0.17), residues: 988 sheet: -0.13 (0.32), residues: 254 loop : -0.71 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 422 HIS 0.002 0.001 HIS B 32 PHE 0.014 0.001 PHE C 694 TYR 0.018 0.001 TYR A 48 ARG 0.006 0.000 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8226 (mm) REVERT: C 493 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7189 (mtt180) outliers start: 45 outliers final: 25 residues processed: 186 average time/residue: 1.6640 time to fit residues: 342.4172 Evaluate side-chains 173 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 493 ARG Chi-restraints excluded: chain C residue 510 ASN Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain C residue 715 ASN Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 41 optimal weight: 0.1980 chunk 122 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 208 optimal weight: 0.5980 chunk 173 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18718 Z= 0.144 Angle : 0.478 11.176 25463 Z= 0.246 Chirality : 0.038 0.154 2841 Planarity : 0.003 0.041 3108 Dihedral : 12.121 177.285 3027 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.20 % Allowed : 21.11 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2137 helix: 1.59 (0.17), residues: 983 sheet: -0.00 (0.32), residues: 254 loop : -0.65 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 49 HIS 0.002 0.000 HIS A 52 PHE 0.014 0.001 PHE C 694 TYR 0.016 0.001 TYR A 48 ARG 0.007 0.000 ARG B 755 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 156 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 MET cc_start: 0.7798 (mmm) cc_final: 0.7572 (tpt) REVERT: C 294 MET cc_start: 0.8556 (ttt) cc_final: 0.8098 (ttt) REVERT: C 493 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7147 (mtt180) outliers start: 41 outliers final: 26 residues processed: 190 average time/residue: 1.7103 time to fit residues: 358.3781 Evaluate side-chains 177 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 493 ARG Chi-restraints excluded: chain C residue 510 ASN Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 208 optimal weight: 0.0060 chunk 130 optimal weight: 0.0570 chunk 126 optimal weight: 0.0010 chunk 96 optimal weight: 0.7980 overall best weight: 0.3520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN B 567 GLN C 715 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18718 Z= 0.127 Angle : 0.466 9.293 25463 Z= 0.240 Chirality : 0.038 0.149 2841 Planarity : 0.003 0.057 3108 Dihedral : 12.079 178.925 3027 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.15 % Allowed : 21.37 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.18), residues: 2137 helix: 1.72 (0.17), residues: 984 sheet: 0.14 (0.33), residues: 254 loop : -0.59 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 49 HIS 0.002 0.000 HIS A 128 PHE 0.013 0.001 PHE C 694 TYR 0.015 0.001 TYR A 48 ARG 0.015 0.000 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 163 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8178 (mm) REVERT: C 294 MET cc_start: 0.8547 (ttt) cc_final: 0.8080 (ttt) REVERT: C 493 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7122 (mtt180) outliers start: 40 outliers final: 19 residues processed: 193 average time/residue: 1.7524 time to fit residues: 373.9733 Evaluate side-chains 167 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 493 ARG Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 0.2980 chunk 102 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 128 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN C 75 GLN C 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18718 Z= 0.347 Angle : 0.575 11.903 25463 Z= 0.296 Chirality : 0.043 0.158 2841 Planarity : 0.004 0.040 3108 Dihedral : 12.162 173.187 3027 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.25 % Allowed : 21.74 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2137 helix: 1.45 (0.16), residues: 984 sheet: 0.03 (0.34), residues: 247 loop : -0.60 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 438 HIS 0.003 0.001 HIS C 285 PHE 0.016 0.002 PHE B 551 TYR 0.026 0.002 TYR A 48 ARG 0.006 0.001 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8229 (mm) REVERT: C 493 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7270 (mtt180) outliers start: 42 outliers final: 23 residues processed: 185 average time/residue: 1.7563 time to fit residues: 356.8920 Evaluate side-chains 176 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 493 ARG Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 116 optimal weight: 0.0270 chunk 84 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 193 optimal weight: 0.0980 chunk 127 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 128 HIS A 346 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN B 532 ASN B 567 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18718 Z= 0.151 Angle : 0.511 11.949 25463 Z= 0.262 Chirality : 0.039 0.151 2841 Planarity : 0.003 0.059 3108 Dihedral : 12.118 178.027 3027 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.31 % Allowed : 22.73 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.18), residues: 2137 helix: 1.65 (0.17), residues: 985 sheet: 0.15 (0.33), residues: 252 loop : -0.53 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 317 HIS 0.002 0.000 HIS A 128 PHE 0.013 0.001 PHE C 694 TYR 0.017 0.001 TYR A 48 ARG 0.019 0.000 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8184 (mm) REVERT: C 294 MET cc_start: 0.8528 (ttt) cc_final: 0.8029 (ttt) REVERT: C 493 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7166 (mtt180) outliers start: 24 outliers final: 17 residues processed: 174 average time/residue: 1.8057 time to fit residues: 346.2976 Evaluate side-chains 167 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 493 ARG Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 132 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18718 Z= 0.205 Angle : 0.531 12.274 25463 Z= 0.270 Chirality : 0.039 0.151 2841 Planarity : 0.004 0.040 3108 Dihedral : 12.108 176.859 3027 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.41 % Allowed : 22.63 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2137 helix: 1.61 (0.17), residues: 989 sheet: 0.17 (0.34), residues: 252 loop : -0.52 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 422 HIS 0.002 0.001 HIS A 128 PHE 0.012 0.001 PHE B 551 TYR 0.029 0.001 TYR A 305 ARG 0.009 0.000 ARG A 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4274 Ramachandran restraints generated. 2137 Oldfield, 0 Emsley, 2137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8207 (mm) REVERT: A 155 MET cc_start: 0.8477 (ttm) cc_final: 0.8246 (ttp) REVERT: C 294 MET cc_start: 0.8533 (ttt) cc_final: 0.8061 (ttt) REVERT: C 493 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7233 (mtt180) outliers start: 26 outliers final: 19 residues processed: 175 average time/residue: 1.8192 time to fit residues: 349.4925 Evaluate side-chains 171 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 493 ARG Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN B 567 GLN C 715 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.082017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.065107 restraints weight = 51113.918| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.20 r_work: 0.2978 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18718 Z= 0.192 Angle : 0.530 12.303 25463 Z= 0.269 Chirality : 0.039 0.150 2841 Planarity : 0.004 0.062 3108 Dihedral : 12.104 177.669 3027 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.62 % Allowed : 22.47 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2137 helix: 1.64 (0.17), residues: 988 sheet: 0.16 (0.33), residues: 259 loop : -0.50 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 422 HIS 0.002 0.001 HIS A 128 PHE 0.011 0.001 PHE A 4 TYR 0.020 0.001 TYR A 48 ARG 0.013 0.000 ARG C 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7357.14 seconds wall clock time: 138 minutes 40.75 seconds (8320.75 seconds total)