Starting phenix.real_space_refine on Fri May 10 03:17:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3k_18871/05_2024/8r3k_18871_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3k_18871/05_2024/8r3k_18871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3k_18871/05_2024/8r3k_18871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3k_18871/05_2024/8r3k_18871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3k_18871/05_2024/8r3k_18871_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3k_18871/05_2024/8r3k_18871_updated.pdb" } resolution = 3.43 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= 0.018 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 45 5.49 5 Mg 2 5.21 5 S 104 5.16 5 C 9143 2.51 5 N 2567 2.21 5 O 2906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 688": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B GLU 697": "OE1" <-> "OE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 14767 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5759 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 708, 5748 Classifications: {'peptide': 708} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 708, 5748 Classifications: {'peptide': 708} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 bond proxies already assigned to first conformer: 5858 Chain: "B" Number of atoms: 5937 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 740, 5925 Classifications: {'peptide': 740} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 709} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 740, 5925 Classifications: {'peptide': 740} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 709} Chain breaks: 1 bond proxies already assigned to first conformer: 6024 Chain: "C" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2024 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain: "V" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 655 Classifications: {'RNA': 31} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna2p': 10, 'rna3p': 20} Chain: "M" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 222 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 1} Link IDs: {'rna3p': 9} Chain: "G" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 159 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 5, 'TRANS': 14} Chain breaks: 1 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} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 559 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 559 " occ=0.50 residue: pdb=" N ATYR B 557 " occ=0.70 ... (22 atoms not shown) pdb=" OH BTYR B 557 " occ=0.30 Time building chain proxies: 13.86, per 1000 atoms: 0.94 Number of scatterers: 14767 At special positions: 0 Unit cell: (113.262, 98.336, 128.188, 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 104 16.00 P 45 15.00 Mg 2 11.99 O 2906 8.00 N 2567 7.00 C 9143 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: 6.93 Conformation dependent library (CDL) restraints added in 4.6 seconds 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3254 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 15 sheets defined 45.1% alpha, 10.6% beta 12 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 6.83 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 11 through 24 removed outlier: 4.523A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) 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 193 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 210 through 217 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 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 434 through 450 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 603 removed outlier: 3.795A pdb=" N MET A 581 " --> pdb=" O TRP A 577 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ARG A 582 " --> pdb=" O GLY A 578 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N CYS A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL A 602 " --> 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: 4.145A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 3.941A 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 18 through 21 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 115 Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.521A pdb=" N GLN B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 152 Processing helix chain 'B' and resid 157 through 160 removed outlier: 3.858A pdb=" N SER B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 160' Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.621A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 246 through 265 removed outlier: 4.455A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 292 Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 315 through 325 Processing helix chain 'B' and resid 331 through 346 removed outlier: 4.660A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.618A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 4.014A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) 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: 4.279A 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 Processing helix chain 'B' and resid 505 through 508 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 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 618 through 624 Processing helix chain 'B' and resid 680 through 699 removed outlier: 4.355A pdb=" N ASP B 685 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU B 686 " --> pdb=" O ILE B 682 " (cutoff:3.500A) 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 22 Processing helix chain 'C' and resid 27 through 33 removed outlier: 3.544A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 61 through 65 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 127 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 76 through 78 removed outlier: 6.681A pdb=" N HIS A 144 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLY A 121 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N HIS A 146 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR A 123 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.372A 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 293 Processing sheet with id= C, first strand: chain 'A' and resid 358 through 360 removed outlier: 4.703A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 619 through 623 removed outlier: 6.702A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (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 181 Processing sheet with id= H, first strand: chain 'B' and resid 184 through 192 Processing sheet with id= I, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.578A pdb=" N MET B 348 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR B 226 " --> pdb=" O MET B 348 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG B 350 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N THR B 228 " --> pdb=" O ARG B 350 " (cutoff:3.500A) 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 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 141 through 148 removed outlier: 6.586A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 7.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4621 1.34 - 1.45: 2287 1.45 - 1.57: 7974 1.57 - 1.69: 91 1.69 - 1.81: 179 Bond restraints: 15152 Sorted by residual: bond pdb=" CG PRO A 28 " pdb=" CD PRO A 28 " ideal model delta sigma weight residual 1.503 1.276 0.227 3.40e-02 8.65e+02 4.47e+01 bond pdb=" N PRO A 28 " pdb=" CD PRO A 28 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" CB PRO A 28 " pdb=" CG PRO A 28 " ideal model delta sigma weight residual 1.492 1.654 -0.162 5.00e-02 4.00e+02 1.05e+01 bond pdb=" O POP B 801 " pdb=" P2 POP B 801 " ideal model delta sigma weight residual 1.661 1.608 0.053 2.00e-02 2.50e+03 7.06e+00 bond pdb=" O POP B 801 " pdb=" P1 POP B 801 " ideal model delta sigma weight residual 1.660 1.608 0.052 2.00e-02 2.50e+03 6.71e+00 ... (remaining 15147 not shown) Histogram of bond angle deviations from ideal: 89.31 - 98.98: 4 98.98 - 108.65: 1154 108.65 - 118.32: 10758 118.32 - 127.99: 8520 127.99 - 137.66: 202 Bond angle restraints: 20638 Sorted by residual: angle pdb=" CA PRO A 28 " pdb=" N PRO A 28 " pdb=" CD PRO A 28 " ideal model delta sigma weight residual 112.00 97.83 14.17 1.40e+00 5.10e-01 1.02e+02 angle pdb=" N PRO A 28 " pdb=" CD PRO A 28 " pdb=" CG PRO A 28 " ideal model delta sigma weight residual 103.20 89.31 13.89 1.50e+00 4.44e-01 8.58e+01 angle pdb=" P1 POP B 801 " pdb=" O POP B 801 " pdb=" P2 POP B 801 " ideal model delta sigma weight residual 139.66 120.47 19.19 3.00e+00 1.11e-01 4.09e+01 angle pdb=" CA PRO A 28 " pdb=" CB PRO A 28 " pdb=" CG PRO A 28 " ideal model delta sigma weight residual 104.50 95.32 9.18 1.90e+00 2.77e-01 2.34e+01 angle pdb=" N LEU B 753 " pdb=" CA LEU B 753 " pdb=" C LEU B 753 " ideal model delta sigma weight residual 110.97 107.16 3.81 1.09e+00 8.42e-01 1.22e+01 ... (remaining 20633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.46: 8798 33.46 - 66.93: 491 66.93 - 100.39: 31 100.39 - 133.86: 1 133.86 - 167.32: 2 Dihedral angle restraints: 9323 sinusoidal: 4298 harmonic: 5025 Sorted by residual: dihedral pdb=" O4' U V 15 " pdb=" C1' U V 15 " pdb=" N1 U V 15 " pdb=" C2 U V 15 " ideal model delta sinusoidal sigma weight residual 200.00 45.92 154.08 1 1.50e+01 4.44e-03 8.10e+01 dihedral pdb=" O4' U V 31 " pdb=" C1' U V 31 " pdb=" N1 U V 31 " pdb=" C2 U V 31 " ideal model delta sinusoidal sigma weight residual -128.00 39.32 -167.32 1 1.70e+01 3.46e-03 6.56e+01 dihedral pdb=" CA ASP A 286 " pdb=" CB ASP A 286 " pdb=" CG ASP A 286 " pdb=" OD1 ASP A 286 " ideal model delta sinusoidal sigma weight residual -30.00 -87.73 57.73 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 9320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1677 0.034 - 0.068: 443 0.068 - 0.102: 107 0.102 - 0.136: 48 0.136 - 0.170: 6 Chirality restraints: 2281 Sorted by residual: chirality pdb=" CA PRO A 28 " pdb=" N PRO A 28 " pdb=" C PRO A 28 " pdb=" CB PRO A 28 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA LEU B 753 " pdb=" N LEU B 753 " pdb=" C LEU B 753 " pdb=" CB LEU B 753 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE B 667 " pdb=" N ILE B 667 " pdb=" C ILE B 667 " pdb=" CB ILE B 667 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 2278 not shown) Planarity restraints: 2502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 27 " 0.049 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO A 28 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 28 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 28 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A 295 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 199 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO C 200 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " -0.026 5.00e-02 4.00e+02 ... (remaining 2499 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 105 2.49 - 3.09: 10786 3.09 - 3.70: 23143 3.70 - 4.30: 34417 4.30 - 4.90: 57453 Nonbonded interactions: 125904 Sorted by model distance: nonbonded pdb=" O2 POP B 801 " pdb="MG MG B 802 " model vdw 1.888 2.170 nonbonded pdb=" OD2 ASP B 305 " pdb="MG MG B 803 " model vdw 2.004 2.170 nonbonded pdb=" OD1 ASP B 445 " pdb="MG MG B 803 " model vdw 2.018 2.170 nonbonded pdb=" OD2 ASP B 522 " pdb=" OH TYR B 559 " model vdw 2.040 2.440 nonbonded pdb=" OD1 ASP B 305 " pdb="MG MG B 802 " model vdw 2.053 2.170 ... (remaining 125899 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=0.30 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: 3.740 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: 0.010 Extract box with map and model: 11.780 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 55.220 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 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 : 0.003 0.227 15152 Z= 0.229 Angle : 0.544 19.191 20638 Z= 0.288 Chirality : 0.036 0.170 2281 Planarity : 0.004 0.068 2502 Dihedral : 18.618 167.320 6069 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 25.85 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.23 (0.21), residues: 1703 helix: 2.00 (0.19), residues: 827 sheet: -0.06 (0.40), residues: 184 loop : -0.36 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 706 HIS 0.003 0.001 HIS A 144 PHE 0.012 0.001 PHE B 740 TYR 0.011 0.001 TYR B 217 ARG 0.010 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.847 Fit side-chains REVERT: B 199 MET cc_start: 0.7630 (mmm) cc_final: 0.7372 (mmm) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.3084 time to fit residues: 105.8340 Evaluate side-chains 224 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 690 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15152 Z= 0.245 Angle : 0.517 7.325 20638 Z= 0.266 Chirality : 0.040 0.143 2281 Planarity : 0.004 0.043 2502 Dihedral : 12.981 171.397 2516 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.95 % Allowed : 24.74 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.13 (0.21), residues: 1703 helix: 1.92 (0.18), residues: 826 sheet: -0.12 (0.39), residues: 185 loop : -0.40 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 706 HIS 0.003 0.001 HIS B 99 PHE 0.012 0.001 PHE B 344 TYR 0.018 0.001 TYR A 130 ARG 0.007 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 227 time to evaluate : 1.713 Fit side-chains revert: symmetry clash REVERT: A 623 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: B 449 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8417 (tt) outliers start: 30 outliers final: 20 residues processed: 247 average time/residue: 0.3244 time to fit residues: 114.4941 Evaluate side-chains 238 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 216 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 126 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN B 567 GLN B 597 ASN B 671 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15152 Z= 0.206 Angle : 0.490 7.079 20638 Z= 0.252 Chirality : 0.039 0.139 2281 Planarity : 0.003 0.038 2502 Dihedral : 12.974 173.768 2516 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.47 % Allowed : 24.80 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.13 (0.20), residues: 1703 helix: 1.92 (0.18), residues: 818 sheet: -0.19 (0.39), residues: 185 loop : -0.36 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 706 HIS 0.003 0.001 HIS A 510 PHE 0.014 0.001 PHE A 191 TYR 0.015 0.001 TYR B 217 ARG 0.006 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 223 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7814 (tm-30) REVERT: A 52 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6296 (m90) REVERT: A 130 TYR cc_start: 0.6881 (t80) cc_final: 0.6537 (t80) REVERT: A 225 SER cc_start: 0.8974 (t) cc_final: 0.8727 (p) REVERT: A 313 THR cc_start: 0.8959 (t) cc_final: 0.8732 (p) REVERT: A 361 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8589 (mmtp) REVERT: A 431 ASP cc_start: 0.7785 (m-30) cc_final: 0.7334 (p0) REVERT: A 593 GLU cc_start: 0.8461 (tt0) cc_final: 0.7982 (tp30) REVERT: A 623 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: B 449 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8415 (tt) REVERT: B 567 GLN cc_start: 0.6499 (OUTLIER) cc_final: 0.6013 (tm130) REVERT: C 11 MET cc_start: 0.8431 (mmm) cc_final: 0.8176 (tpp) outliers start: 38 outliers final: 23 residues processed: 249 average time/residue: 0.3211 time to fit residues: 114.6397 Evaluate side-chains 242 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 215 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN B 567 GLN B 671 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15152 Z= 0.218 Angle : 0.488 7.068 20638 Z= 0.250 Chirality : 0.039 0.138 2281 Planarity : 0.003 0.035 2502 Dihedral : 12.980 174.136 2516 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.54 % Allowed : 24.61 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.08 (0.20), residues: 1703 helix: 1.88 (0.18), residues: 818 sheet: -0.21 (0.38), residues: 185 loop : -0.38 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 706 HIS 0.003 0.001 HIS A 144 PHE 0.013 0.001 PHE B 344 TYR 0.015 0.001 TYR B 217 ARG 0.010 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 221 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 52 HIS cc_start: 0.7074 (OUTLIER) cc_final: 0.6286 (m90) REVERT: A 130 TYR cc_start: 0.6874 (t80) cc_final: 0.6523 (t80) REVERT: A 225 SER cc_start: 0.8981 (t) cc_final: 0.8732 (p) REVERT: A 361 LYS cc_start: 0.8847 (mmtt) cc_final: 0.8596 (mmtp) REVERT: A 372 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: A 431 ASP cc_start: 0.7793 (m-30) cc_final: 0.7405 (p0) REVERT: A 593 GLU cc_start: 0.8499 (tt0) cc_final: 0.8011 (tp30) REVERT: A 623 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: B 449 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8438 (tt) REVERT: B 567 GLN cc_start: 0.6357 (OUTLIER) cc_final: 0.6106 (tm-30) REVERT: C 187 LYS cc_start: 0.8300 (ptmt) cc_final: 0.8010 (ptmt) outliers start: 39 outliers final: 29 residues processed: 249 average time/residue: 0.3140 time to fit residues: 111.6738 Evaluate side-chains 252 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 218 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 42 optimal weight: 0.0570 chunk 56 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN B 567 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15152 Z= 0.179 Angle : 0.473 6.947 20638 Z= 0.243 Chirality : 0.038 0.138 2281 Planarity : 0.003 0.035 2502 Dihedral : 12.978 174.749 2516 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.06 % Allowed : 24.02 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.03 (0.20), residues: 1703 helix: 1.88 (0.18), residues: 822 sheet: -0.22 (0.38), residues: 185 loop : -0.47 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 706 HIS 0.003 0.001 HIS A 510 PHE 0.011 0.001 PHE B 344 TYR 0.014 0.001 TYR B 217 ARG 0.008 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 222 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7769 (tm-30) REVERT: A 52 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.6314 (m90) REVERT: A 114 GLU cc_start: 0.7128 (tt0) cc_final: 0.6923 (tt0) REVERT: A 130 TYR cc_start: 0.6870 (t80) cc_final: 0.6495 (t80) REVERT: A 187 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5745 (pp) REVERT: A 225 SER cc_start: 0.8967 (t) cc_final: 0.8731 (p) REVERT: A 313 THR cc_start: 0.8904 (t) cc_final: 0.8694 (p) REVERT: A 361 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8612 (mmtp) REVERT: A 372 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: A 431 ASP cc_start: 0.7779 (m-30) cc_final: 0.7401 (p0) REVERT: A 593 GLU cc_start: 0.8488 (tt0) cc_final: 0.7707 (tp30) REVERT: A 623 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: B 449 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8411 (tt) REVERT: B 567 GLN cc_start: 0.6257 (OUTLIER) cc_final: 0.5883 (tm-30) REVERT: C 11 MET cc_start: 0.8369 (mmm) cc_final: 0.8075 (tpp) REVERT: C 187 LYS cc_start: 0.8252 (ptmt) cc_final: 0.7967 (ptmt) outliers start: 47 outliers final: 30 residues processed: 258 average time/residue: 0.3038 time to fit residues: 113.4446 Evaluate side-chains 251 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 215 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 567 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15152 Z= 0.209 Angle : 0.487 7.164 20638 Z= 0.249 Chirality : 0.038 0.165 2281 Planarity : 0.003 0.035 2502 Dihedral : 12.982 174.898 2516 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.86 % Allowed : 24.87 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 0.97 (0.20), residues: 1703 helix: 1.81 (0.18), residues: 823 sheet: -0.23 (0.38), residues: 185 loop : -0.49 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 706 HIS 0.003 0.001 HIS A 510 PHE 0.013 0.001 PHE B 344 TYR 0.014 0.001 TYR B 217 ARG 0.005 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 225 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 52 HIS cc_start: 0.7051 (OUTLIER) cc_final: 0.6279 (m90) REVERT: A 101 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7225 (mt-10) REVERT: A 114 GLU cc_start: 0.7187 (tt0) cc_final: 0.6980 (tt0) REVERT: A 130 TYR cc_start: 0.6871 (t80) cc_final: 0.6507 (t80) REVERT: A 187 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5769 (pp) REVERT: A 225 SER cc_start: 0.8978 (t) cc_final: 0.8738 (p) REVERT: A 313 THR cc_start: 0.8905 (t) cc_final: 0.8697 (p) REVERT: A 361 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8644 (mmtp) REVERT: A 372 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: A 431 ASP cc_start: 0.7785 (m-30) cc_final: 0.7445 (p0) REVERT: A 593 GLU cc_start: 0.8494 (tt0) cc_final: 0.8000 (tp30) REVERT: A 623 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: B 237 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8350 (mtmt) REVERT: B 449 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8454 (tt) REVERT: B 567 GLN cc_start: 0.6017 (OUTLIER) cc_final: 0.5641 (tm-30) REVERT: C 11 MET cc_start: 0.8323 (mmm) cc_final: 0.8028 (tpp) REVERT: C 46 ARG cc_start: 0.7923 (ttt90) cc_final: 0.7591 (ttm170) REVERT: C 187 LYS cc_start: 0.8247 (ptmt) cc_final: 0.7964 (ptmt) outliers start: 44 outliers final: 34 residues processed: 259 average time/residue: 0.3061 time to fit residues: 113.6294 Evaluate side-chains 260 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 218 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 103 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.8461 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15152 Z= 0.175 Angle : 0.478 7.124 20638 Z= 0.245 Chirality : 0.038 0.160 2281 Planarity : 0.003 0.046 2502 Dihedral : 12.984 175.344 2516 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.19 % Allowed : 25.00 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.03 (0.20), residues: 1703 helix: 1.86 (0.18), residues: 824 sheet: -0.22 (0.38), residues: 185 loop : -0.46 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 706 HIS 0.003 0.001 HIS A 510 PHE 0.012 0.001 PHE B 344 TYR 0.013 0.001 TYR B 217 ARG 0.006 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 220 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7722 (tm-30) REVERT: A 52 HIS cc_start: 0.7023 (OUTLIER) cc_final: 0.6284 (m90) REVERT: A 101 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7210 (mt-10) REVERT: A 114 GLU cc_start: 0.7197 (tt0) cc_final: 0.6991 (tt0) REVERT: A 130 TYR cc_start: 0.6860 (t80) cc_final: 0.6488 (t80) REVERT: A 187 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5779 (pp) REVERT: A 225 SER cc_start: 0.8944 (t) cc_final: 0.8726 (p) REVERT: A 372 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: A 431 ASP cc_start: 0.7759 (m-30) cc_final: 0.7432 (p0) REVERT: A 593 GLU cc_start: 0.8481 (tt0) cc_final: 0.7740 (tp30) REVERT: A 623 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: B 237 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8338 (mtmt) REVERT: B 449 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8361 (tt) REVERT: C 11 MET cc_start: 0.8312 (mmm) cc_final: 0.8023 (tpp) REVERT: C 187 LYS cc_start: 0.8239 (ptmt) cc_final: 0.7960 (ptmt) outliers start: 49 outliers final: 35 residues processed: 257 average time/residue: 0.2994 time to fit residues: 111.6525 Evaluate side-chains 254 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 212 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 152 optimal weight: 0.0030 chunk 160 optimal weight: 0.9980 chunk 146 optimal weight: 0.4980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN B 671 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15152 Z= 0.184 Angle : 0.481 6.903 20638 Z= 0.247 Chirality : 0.038 0.159 2281 Planarity : 0.003 0.034 2502 Dihedral : 12.944 171.429 2516 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.06 % Allowed : 25.20 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.01 (0.20), residues: 1703 helix: 1.83 (0.18), residues: 824 sheet: -0.20 (0.38), residues: 185 loop : -0.46 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 706 HIS 0.003 0.001 HIS A 510 PHE 0.013 0.001 PHE B 344 TYR 0.013 0.001 TYR B 217 ARG 0.006 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 219 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 52 HIS cc_start: 0.7029 (OUTLIER) cc_final: 0.6288 (m90) REVERT: A 101 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7208 (mt-10) REVERT: A 114 GLU cc_start: 0.7263 (tt0) cc_final: 0.7059 (tt0) REVERT: A 130 TYR cc_start: 0.6857 (t80) cc_final: 0.6471 (t80) REVERT: A 187 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5796 (pp) REVERT: A 225 SER cc_start: 0.8946 (t) cc_final: 0.8733 (p) REVERT: A 372 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: A 431 ASP cc_start: 0.7739 (m-30) cc_final: 0.7460 (p0) REVERT: A 593 GLU cc_start: 0.8477 (tt0) cc_final: 0.7837 (tp30) REVERT: A 623 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: B 237 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8348 (mtmt) REVERT: B 449 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8323 (tt) REVERT: C 11 MET cc_start: 0.8299 (mmm) cc_final: 0.8029 (tpp) outliers start: 47 outliers final: 36 residues processed: 254 average time/residue: 0.3037 time to fit residues: 111.1591 Evaluate side-chains 258 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 215 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8463 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.202 15152 Z= 0.249 Angle : 0.720 59.195 20638 Z= 0.418 Chirality : 0.039 0.208 2281 Planarity : 0.003 0.035 2502 Dihedral : 12.946 171.432 2516 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.99 % Allowed : 25.07 % Favored : 71.94 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.25 % 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: 1.01 (0.20), residues: 1703 helix: 1.83 (0.18), residues: 824 sheet: -0.20 (0.38), residues: 185 loop : -0.45 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 706 HIS 0.003 0.001 HIS A 510 PHE 0.012 0.001 PHE B 344 TYR 0.012 0.001 TYR B 217 ARG 0.005 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 215 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 52 HIS cc_start: 0.7026 (OUTLIER) cc_final: 0.6284 (m90) REVERT: A 101 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: A 130 TYR cc_start: 0.6857 (t80) cc_final: 0.6471 (t80) REVERT: A 187 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5775 (pp) REVERT: A 225 SER cc_start: 0.8945 (t) cc_final: 0.8735 (p) REVERT: A 372 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: A 431 ASP cc_start: 0.7739 (m-30) cc_final: 0.7462 (p0) REVERT: A 593 GLU cc_start: 0.8479 (tt0) cc_final: 0.7838 (tp30) REVERT: A 623 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: B 237 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8348 (mtmt) REVERT: B 449 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8326 (tt) REVERT: C 11 MET cc_start: 0.8315 (mmm) cc_final: 0.8031 (tpp) outliers start: 46 outliers final: 38 residues processed: 251 average time/residue: 0.3038 time to fit residues: 110.1430 Evaluate side-chains 257 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 212 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 106 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 147 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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: 0.8463 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.202 15152 Z= 0.249 Angle : 0.720 59.195 20638 Z= 0.418 Chirality : 0.039 0.208 2281 Planarity : 0.003 0.035 2502 Dihedral : 12.946 171.432 2516 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.93 % Allowed : 25.26 % Favored : 71.81 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.25 % 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: 1.01 (0.20), residues: 1703 helix: 1.83 (0.18), residues: 824 sheet: -0.20 (0.38), residues: 185 loop : -0.45 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 706 HIS 0.003 0.001 HIS A 510 PHE 0.012 0.001 PHE B 344 TYR 0.012 0.001 TYR B 217 ARG 0.005 0.000 ARG B 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 212 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 52 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.6284 (m90) REVERT: A 101 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: A 130 TYR cc_start: 0.6859 (t80) cc_final: 0.6472 (t80) REVERT: A 187 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5775 (pp) REVERT: A 225 SER cc_start: 0.8945 (t) cc_final: 0.8735 (p) REVERT: A 372 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: A 431 ASP cc_start: 0.7740 (m-30) cc_final: 0.7462 (p0) REVERT: A 593 GLU cc_start: 0.8480 (tt0) cc_final: 0.7838 (tp30) REVERT: A 623 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: B 237 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8348 (mtmt) REVERT: B 449 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8326 (tt) REVERT: C 11 MET cc_start: 0.8318 (mmm) cc_final: 0.8031 (tpp) outliers start: 45 outliers final: 38 residues processed: 247 average time/residue: 0.2951 time to fit residues: 105.3344 Evaluate side-chains 257 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 212 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.0070 chunk 127 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 138 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 141 optimal weight: 0.0770 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109766 restraints weight = 44875.465| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.69 r_work: 0.3078 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.202 15152 Z= 0.249 Angle : 0.720 59.195 20638 Z= 0.418 Chirality : 0.039 0.208 2281 Planarity : 0.003 0.035 2502 Dihedral : 12.946 171.432 2516 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.93 % Allowed : 25.26 % Favored : 71.81 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.25 % 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: 1.01 (0.20), residues: 1703 helix: 1.83 (0.18), residues: 824 sheet: -0.20 (0.38), residues: 185 loop : -0.45 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 706 HIS 0.003 0.001 HIS A 510 PHE 0.012 0.001 PHE B 344 TYR 0.012 0.001 TYR B 217 ARG 0.005 0.000 ARG B 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3473.47 seconds wall clock time: 64 minutes 22.65 seconds (3862.65 seconds total)