Starting phenix.real_space_refine (version: dev) on Tue Feb 21 17:37:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szu_10354/02_2023/6szu_10354_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szu_10354/02_2023/6szu_10354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szu_10354/02_2023/6szu_10354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szu_10354/02_2023/6szu_10354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szu_10354/02_2023/6szu_10354_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szu_10354/02_2023/6szu_10354_updated.pdb" } resolution = 2.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 Process input model Symmetric amino acids flipped Residue "A GLU 64": "OE1" <-> "OE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 571": "NH1" <-> "NH2" Residue "B PHE 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 707": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15245 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 705, 5750 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 25, 'TRANS': 679} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 705, 5750 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 25, 'TRANS': 679} Chain breaks: 2 bond proxies already assigned to first conformer: 5860 Chain: "B" Number of atoms: 5964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5964 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 716} Chain breaks: 1 Chain: "C" Number of atoms: 2022 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 249, 2012 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 249, 2012 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} bond proxies already assigned to first conformer: 2040 Chain: "V" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 929 Classifications: {'RNA': 44} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 12, 'rna3p_pyr': 15} Link IDs: {'rna2p': 17, 'rna3p': 26} Chain: "M" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 217 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' MG': 2, 'M4H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 2, 'POP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "B" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 136 Classifications: {'water': 136} Link IDs: {None: 135} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "V" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "M" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 491 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 491 " occ=0.50 residue: pdb=" N AHIS C 27 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 27 " occ=0.50 Time building chain proxies: 12.61, per 1000 atoms: 0.83 Number of scatterers: 15245 At special positions: 0 Unit cell: (97.524, 119.467, 117.841, 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 92 16.00 P 56 15.00 Mg 6 11.99 O 3273 8.00 N 2605 7.00 C 9213 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=0, symmetry=0 Time building additional restraints: 6.72 Conformation dependent library (CDL) restraints added in 3.1 seconds 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 16 sheets defined 44.8% alpha, 11.5% beta 12 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 5.62 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.709A pdb=" N GLN A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) 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 313 removed outlier: 3.785A pdb=" N THR A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 346 Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 429 through 445 removed outlier: 3.646A pdb=" N PHE A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 470 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 529 through 532 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 576 through 598 removed outlier: 3.955A pdb=" N SER A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN A 585 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 588 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 594 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 598 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 628 through 644 Processing helix chain 'A' and resid 648 through 668 removed outlier: 3.970A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 693 through 713 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.578A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.785A pdb=" N GLN B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) 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: 3.926A pdb=" N PHE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU B 175 " --> pdb=" O LEU 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: 4.038A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 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: 3.681A pdb=" N VAL B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix 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 removed outlier: 5.312A pdb=" N HIS B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU B 395 " --> pdb=" O LYS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.068A pdb=" N GLY B 427 " --> pdb=" O VAL 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 472 Processing helix chain 'B' and resid 505 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 558 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 608 through 611 No H-bonds generated for 'chain 'B' and resid 608 through 611' Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 680 through 696 removed outlier: 5.400A pdb=" N ASP B 685 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU B 686 " --> pdb=" O ILE B 682 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B 687 " --> pdb=" O LEU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 731 Processing helix chain 'B' and resid 737 through 755 Processing helix chain 'C' and resid 1 through 12 Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 25 through 32 removed outlier: 3.818A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL 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 sheet with id= A, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= B, first strand: chain 'A' and resid 76 through 78 Processing sheet with id= C, first strand: chain 'A' and resid 290 through 293 Processing sheet with id= D, first strand: chain 'A' and resid 477 through 479 removed outlier: 6.460A pdb=" N LEU A 558 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLU A 539 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 560 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VAL A 537 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A 539 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE A 322 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 614 through 619 removed outlier: 6.578A pdb=" N GLU A 624 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU A 618 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= G, first strand: chain 'B' and resid 127 through 130 Processing sheet with id= H, first strand: chain 'B' and resid 178 through 192 Processing sheet with id= I, first strand: chain 'B' and resid 224 through 228 Processing sheet with id= J, first strand: chain 'B' and resid 483 through 486 Processing sheet with id= K, first strand: chain 'B' and resid 348 through 350 Processing sheet with id= L, first strand: chain 'B' and resid 355 through 359 Processing sheet with id= M, first strand: chain 'B' and resid 489 through 492 Processing sheet with id= N, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= O, first strand: chain 'C' and resid 133 through 135 Processing sheet with id= P, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.419A pdb=" N ARG C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 5.48 Time building geometry restraints manager: 7.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3139 1.33 - 1.45: 3674 1.45 - 1.57: 8260 1.57 - 1.69: 108 1.69 - 1.81: 160 Bond restraints: 15341 Sorted by residual: bond pdb=" C19 M4H A 801 " pdb=" C20 M4H A 801 " ideal model delta sigma weight residual 1.414 1.464 -0.050 2.00e-02 2.50e+03 6.18e+00 bond pdb=" C1 M4H A 801 " pdb=" C6 M4H A 801 " ideal model delta sigma weight residual 1.437 1.481 -0.044 2.00e-02 2.50e+03 4.75e+00 bond pdb=" C13 M4H A 801 " pdb=" N18 M4H A 801 " ideal model delta sigma weight residual 1.459 1.498 -0.039 2.00e-02 2.50e+03 3.84e+00 bond pdb=" CB ARG B 135 " pdb=" CG ARG B 135 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.40e+00 bond pdb=" CG1 ILE B 606 " pdb=" CD1 ILE B 606 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.32e+00 ... (remaining 15336 not shown) Histogram of bond angle deviations from ideal: 97.12 - 105.58: 524 105.58 - 114.04: 8865 114.04 - 122.50: 9427 122.50 - 130.96: 2053 130.96 - 139.41: 80 Bond angle restraints: 20949 Sorted by residual: angle pdb=" N ILE A 79 " pdb=" CA ILE A 79 " pdb=" C ILE A 79 " ideal model delta sigma weight residual 112.96 107.05 5.91 1.00e+00 1.00e+00 3.50e+01 angle pdb=" N18 M4H A 801 " pdb=" C19 M4H A 801 " pdb=" N26 M4H A 801 " ideal model delta sigma weight residual 125.81 139.41 -13.60 3.00e+00 1.11e-01 2.06e+01 angle pdb=" O4' A V 7 " pdb=" C1' A V 7 " pdb=" N9 A V 7 " ideal model delta sigma weight residual 108.20 113.95 -5.75 1.50e+00 4.44e-01 1.47e+01 angle pdb=" C ASN B 628 " pdb=" N ASN B 629 " pdb=" CA ASN B 629 " ideal model delta sigma weight residual 121.80 131.07 -9.27 2.44e+00 1.68e-01 1.44e+01 angle pdb=" C MET B 407 " pdb=" N MET B 408 " pdb=" CA MET B 408 " ideal model delta sigma weight residual 121.54 128.45 -6.91 1.91e+00 2.74e-01 1.31e+01 ... (remaining 20944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.80: 8311 18.80 - 37.59: 673 37.59 - 56.39: 174 56.39 - 75.18: 45 75.18 - 93.98: 16 Dihedral angle restraints: 9219 sinusoidal: 4249 harmonic: 4970 Sorted by residual: dihedral pdb=" CA VAL A 512 " pdb=" C VAL A 512 " pdb=" N VAL A 513 " pdb=" CA VAL A 513 " ideal model delta harmonic sigma weight residual 180.00 155.85 24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ILE A 481 " pdb=" C ILE A 481 " pdb=" N THR A 482 " pdb=" CA THR A 482 " ideal model delta harmonic sigma weight residual 180.00 156.20 23.80 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ASN B 134 " pdb=" C ASN B 134 " pdb=" N ARG B 135 " pdb=" CA ARG B 135 " ideal model delta harmonic sigma weight residual -180.00 -157.02 -22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 9216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1712 0.057 - 0.113: 531 0.113 - 0.170: 76 0.170 - 0.226: 5 0.226 - 0.283: 1 Chirality restraints: 2325 Sorted by residual: chirality pdb=" C1' A V 7 " pdb=" O4' A V 7 " pdb=" C2' A V 7 " pdb=" N9 A V 7 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C1' A V 4 " pdb=" O4' A V 4 " pdb=" C2' A V 4 " pdb=" N9 A V 4 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE B 392 " pdb=" CA ILE B 392 " pdb=" CG1 ILE B 392 " pdb=" CG2 ILE B 392 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2322 not shown) Planarity restraints: 2493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.046 2.00e-02 2.50e+03 1.99e-02 1.09e+01 pdb=" N9 A V 7 " 0.040 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A V 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.012 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.010 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.010 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 10 " 0.047 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO A 11 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 11 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 11 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 557 " -0.036 2.00e-02 2.50e+03 1.92e-02 7.41e+00 pdb=" CG TYR B 557 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 557 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 557 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 557 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 557 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 557 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 557 " -0.014 2.00e-02 2.50e+03 ... (remaining 2490 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 279 2.59 - 3.17: 11939 3.17 - 3.75: 26716 3.75 - 4.32: 39267 4.32 - 4.90: 59228 Nonbonded interactions: 137429 Sorted by model distance: nonbonded pdb=" OD2 ASP A 108 " pdb="MG MG A 803 " model vdw 2.013 2.170 nonbonded pdb=" O11 M4H A 801 " pdb="MG MG A 803 " model vdw 2.026 2.170 nonbonded pdb=" OD1 ASP A 108 " pdb="MG MG A 802 " model vdw 2.027 2.170 nonbonded pdb=" O8 M4H A 801 " pdb="MG MG A 802 " model vdw 2.039 2.170 nonbonded pdb=" O10 M4H A 801 " pdb="MG MG A 803 " model vdw 2.090 2.170 ... (remaining 137424 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 56 5.49 5 Mg 6 5.21 5 S 92 5.16 5 C 9213 2.51 5 N 2605 2.21 5 O 3273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.740 Check model and map are aligned: 0.220 Process input model: 50.950 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 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 : 0.008 0.084 15341 Z= 0.484 Angle : 0.825 13.604 20949 Z= 0.459 Chirality : 0.052 0.283 2325 Planarity : 0.006 0.072 2493 Dihedral : 15.378 93.978 6003 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.21 % Favored : 95.67 % Rotamer Outliers : 5.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -2.10 (0.17), residues: 1693 helix: -1.43 (0.14), residues: 815 sheet: -0.78 (0.35), residues: 173 loop : -1.30 (0.20), residues: 705 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 240 time to evaluate : 1.585 Fit side-chains outliers start: 80 outliers final: 32 residues processed: 303 average time/residue: 1.7844 time to fit residues: 581.7301 Evaluate side-chains 245 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 213 time to evaluate : 1.703 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 6 average time/residue: 0.7873 time to fit residues: 7.8739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN A 254 ASN A 425 ASN A 582 GLN B 134 ASN B 137 GLN B 202 GLN B 633 HIS C 27 HIS A C 75 ASN C 233 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 15341 Z= 0.163 Angle : 0.504 6.160 20949 Z= 0.272 Chirality : 0.039 0.208 2325 Planarity : 0.004 0.056 2493 Dihedral : 8.622 86.395 2511 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 3.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.50 (0.19), residues: 1693 helix: 0.23 (0.17), residues: 812 sheet: -0.41 (0.37), residues: 172 loop : -0.86 (0.22), residues: 709 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 215 time to evaluate : 1.926 Fit side-chains outliers start: 54 outliers final: 22 residues processed: 260 average time/residue: 1.7250 time to fit residues: 485.3972 Evaluate side-chains 222 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 200 time to evaluate : 1.707 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 2 average time/residue: 0.3037 time to fit residues: 3.2458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN B 413 ASN B 633 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 15341 Z= 0.360 Angle : 0.624 6.447 20949 Z= 0.332 Chirality : 0.045 0.240 2325 Planarity : 0.005 0.049 2493 Dihedral : 8.856 89.777 2511 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 3.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.05 (0.20), residues: 1693 helix: 0.64 (0.18), residues: 812 sheet: -0.38 (0.35), residues: 181 loop : -0.61 (0.22), residues: 700 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 203 time to evaluate : 1.663 Fit side-chains outliers start: 57 outliers final: 29 residues processed: 245 average time/residue: 1.6844 time to fit residues: 446.4932 Evaluate side-chains 237 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 208 time to evaluate : 1.822 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 23 residues processed: 6 average time/residue: 0.5069 time to fit residues: 6.2463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 0.0770 chunk 45 optimal weight: 3.9990 overall best weight: 1.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN B 176 ASN B 567 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 15341 Z= 0.169 Angle : 0.506 6.771 20949 Z= 0.271 Chirality : 0.039 0.205 2325 Planarity : 0.004 0.044 2493 Dihedral : 8.519 85.427 2511 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.20), residues: 1693 helix: 1.01 (0.18), residues: 813 sheet: -0.18 (0.38), residues: 173 loop : -0.52 (0.22), residues: 707 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 204 time to evaluate : 1.913 Fit side-chains outliers start: 45 outliers final: 24 residues processed: 239 average time/residue: 1.6798 time to fit residues: 436.6581 Evaluate side-chains 225 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 201 time to evaluate : 1.724 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 23 residues processed: 1 average time/residue: 0.1985 time to fit residues: 2.4728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 15341 Z= 0.250 Angle : 0.556 8.824 20949 Z= 0.295 Chirality : 0.042 0.211 2325 Planarity : 0.004 0.041 2493 Dihedral : 8.565 85.936 2511 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.40 (0.20), residues: 1693 helix: 1.06 (0.18), residues: 811 sheet: -0.25 (0.37), residues: 178 loop : -0.44 (0.22), residues: 704 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 201 time to evaluate : 1.841 Fit side-chains outliers start: 48 outliers final: 31 residues processed: 238 average time/residue: 1.6539 time to fit residues: 428.0523 Evaluate side-chains 231 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 200 time to evaluate : 1.746 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 26 residues processed: 5 average time/residue: 0.2345 time to fit residues: 4.2545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 15341 Z= 0.165 Angle : 0.500 8.771 20949 Z= 0.266 Chirality : 0.039 0.203 2325 Planarity : 0.003 0.040 2493 Dihedral : 8.389 84.913 2511 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1693 helix: 1.19 (0.19), residues: 813 sheet: -0.18 (0.37), residues: 180 loop : -0.37 (0.23), residues: 700 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 203 time to evaluate : 1.774 Fit side-chains outliers start: 41 outliers final: 26 residues processed: 238 average time/residue: 1.7036 time to fit residues: 439.3680 Evaluate side-chains 228 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 202 time to evaluate : 1.701 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 2 average time/residue: 0.2620 time to fit residues: 3.1437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 166 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 15341 Z= 0.289 Angle : 0.576 8.647 20949 Z= 0.306 Chirality : 0.043 0.230 2325 Planarity : 0.004 0.040 2493 Dihedral : 8.559 86.104 2511 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.44 (0.20), residues: 1693 helix: 1.07 (0.18), residues: 811 sheet: -0.22 (0.37), residues: 178 loop : -0.39 (0.22), residues: 704 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 203 time to evaluate : 1.831 Fit side-chains outliers start: 42 outliers final: 28 residues processed: 237 average time/residue: 1.6808 time to fit residues: 432.8100 Evaluate side-chains 230 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 time to evaluate : 1.630 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 0.2498 time to fit residues: 3.7830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 151 optimal weight: 0.0980 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 15341 Z= 0.221 Angle : 0.535 8.675 20949 Z= 0.285 Chirality : 0.041 0.228 2325 Planarity : 0.004 0.039 2493 Dihedral : 8.476 85.857 2511 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.49 (0.20), residues: 1693 helix: 1.12 (0.18), residues: 813 sheet: -0.20 (0.37), residues: 180 loop : -0.36 (0.22), residues: 700 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 202 time to evaluate : 1.899 Fit side-chains outliers start: 36 outliers final: 25 residues processed: 229 average time/residue: 1.8028 time to fit residues: 448.4495 Evaluate side-chains 228 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 1.731 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 24 residues processed: 1 average time/residue: 0.3121 time to fit residues: 2.8219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 15341 Z= 0.320 Angle : 0.599 8.604 20949 Z= 0.318 Chirality : 0.044 0.240 2325 Planarity : 0.005 0.042 2493 Dihedral : 8.621 86.958 2511 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.37 (0.20), residues: 1693 helix: 0.98 (0.18), residues: 813 sheet: -0.25 (0.36), residues: 181 loop : -0.39 (0.22), residues: 699 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 202 time to evaluate : 1.897 Fit side-chains outliers start: 37 outliers final: 27 residues processed: 228 average time/residue: 1.6750 time to fit residues: 414.0480 Evaluate side-chains 228 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 201 time to evaluate : 1.760 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 24 residues processed: 3 average time/residue: 0.2355 time to fit residues: 3.5562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 77 optimal weight: 0.0470 chunk 114 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 15341 Z= 0.154 Angle : 0.492 8.873 20949 Z= 0.263 Chirality : 0.039 0.202 2325 Planarity : 0.003 0.039 2493 Dihedral : 8.338 84.651 2511 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.53 (0.20), residues: 1693 helix: 1.15 (0.18), residues: 827 sheet: -0.14 (0.37), residues: 180 loop : -0.40 (0.23), residues: 686 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 1.935 Fit side-chains outliers start: 26 outliers final: 23 residues processed: 229 average time/residue: 1.7190 time to fit residues: 427.2999 Evaluate side-chains 223 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 2.4420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.145681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.113419 restraints weight = 16252.344| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.21 r_work: 0.2989 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 15341 Z= 0.199 Angle : 0.521 8.854 20949 Z= 0.277 Chirality : 0.040 0.200 2325 Planarity : 0.004 0.038 2493 Dihedral : 8.368 84.660 2511 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.62 (0.20), residues: 1693 helix: 1.21 (0.18), residues: 813 sheet: -0.13 (0.37), residues: 178 loop : -0.28 (0.23), residues: 702 =============================================================================== Job complete usr+sys time: 6824.90 seconds wall clock time: 121 minutes 29.54 seconds (7289.54 seconds total)