Starting phenix.real_space_refine on Mon Mar 18 01:54:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/03_2024/5o9g_3765_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/03_2024/5o9g_3765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/03_2024/5o9g_3765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/03_2024/5o9g_3765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/03_2024/5o9g_3765_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/03_2024/5o9g_3765_neut_updated.pdb" } resolution = 4.8 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 325 5.49 5 S 39 5.16 5 Be 1 3.05 5 C 11400 2.51 5 N 3594 2.21 5 O 4319 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 45": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "W TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 807": "NH1" <-> "NH2" Residue "W PHE 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19681 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 697 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3304 Classifications: {'DNA': 162} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 161} Chain: "J" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3335 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "W" Number of atoms: 7048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 857, 7048 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'peptide': 855, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 29, 'TRANS': 825, None: 2} Not linked: pdbres="GLY W1266 " pdbres="ADP W1501 " Not linked: pdbres="ADP W1501 " pdbres="BEF W1502 " Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.27, per 1000 atoms: 0.47 Number of scatterers: 19681 At special positions: 0 Unit cell: (131.52, 190.43, 138.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 39 16.00 P 325 15.00 F 3 9.00 O 4319 8.00 N 3594 7.00 C 11400 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.04 Conformation dependent library (CDL) restraints added in 2.4 seconds 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3044 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 6 sheets defined 52.6% alpha, 3.9% beta 161 base pairs and 249 stacking pairs defined. Time for finding SS restraints: 28.42 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 64 through 78 Processing helix chain 'A' and resid 86 through 113 removed outlier: 3.908A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 51 through 75 removed outlier: 3.612A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 47 through 72 Processing helix chain 'C' and resid 80 through 87 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 120 Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 78 Processing helix chain 'E' and resid 86 through 113 removed outlier: 3.872A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE E 104 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 51 through 76 removed outlier: 3.860A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 71 Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 36 through 42 removed outlier: 3.685A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 102 through 120 Processing helix chain 'W' and resid 204 through 209 Processing helix chain 'W' and resid 222 through 224 No H-bonds generated for 'chain 'W' and resid 222 through 224' Processing helix chain 'W' and resid 240 through 256 Processing helix chain 'W' and resid 265 through 284 removed outlier: 3.691A pdb=" N ARG W 274 " --> pdb=" O MET W 270 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU W 275 " --> pdb=" O ASP W 271 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU W 283 " --> pdb=" O ASP W 279 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE W 284 " --> pdb=" O GLU W 280 " (cutoff:3.500A) Processing helix chain 'W' and resid 332 through 343 removed outlier: 3.543A pdb=" N GLU W 342 " --> pdb=" O PHE W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 350 No H-bonds generated for 'chain 'W' and resid 348 through 350' Processing helix chain 'W' and resid 379 through 393 removed outlier: 4.268A pdb=" N LYS W 393 " --> pdb=" O PHE W 389 " (cutoff:3.500A) Processing helix chain 'W' and resid 407 through 420 Processing helix chain 'W' and resid 434 through 447 Proline residue: W 438 - end of helix Processing helix chain 'W' and resid 461 through 470 Processing helix chain 'W' and resid 492 through 497 removed outlier: 3.586A pdb=" N LEU W 496 " --> pdb=" O TYR W 492 " (cutoff:3.500A) Processing helix chain 'W' and resid 500 through 503 No H-bonds generated for 'chain 'W' and resid 500 through 503' Processing helix chain 'W' and resid 515 through 519 removed outlier: 3.790A pdb=" N LEU W 518 " --> pdb=" O ALA W 515 " (cutoff:3.500A) Processing helix chain 'W' and resid 524 through 529 Processing helix chain 'W' and resid 549 through 559 removed outlier: 4.073A pdb=" N LEU W 559 " --> pdb=" O LEU W 555 " (cutoff:3.500A) Processing helix chain 'W' and resid 579 through 593 removed outlier: 4.284A pdb=" N ARG W 588 " --> pdb=" O HIS W 584 " (cutoff:3.500A) Proline residue: W 592 - end of helix Processing helix chain 'W' and resid 599 through 601 No H-bonds generated for 'chain 'W' and resid 599 through 601' Processing helix chain 'W' and resid 603 through 605 No H-bonds generated for 'chain 'W' and resid 603 through 605' Processing helix chain 'W' and resid 620 through 627 Processing helix chain 'W' and resid 653 through 659 Processing helix chain 'W' and resid 669 through 672 No H-bonds generated for 'chain 'W' and resid 669 through 672' Processing helix chain 'W' and resid 684 through 691 Processing helix chain 'W' and resid 695 through 708 Processing helix chain 'W' and resid 721 through 730 removed outlier: 3.625A pdb=" N ASP W 725 " --> pdb=" O VAL W 721 " (cutoff:3.500A) Processing helix chain 'W' and resid 747 through 757 removed outlier: 3.892A pdb=" N ILE W 752 " --> pdb=" O ALA W 748 " (cutoff:3.500A) Processing helix chain 'W' and resid 797 through 804 removed outlier: 3.916A pdb=" N ARG W 804 " --> pdb=" O GLN W 800 " (cutoff:3.500A) Processing helix chain 'W' and resid 826 through 835 Processing helix chain 'W' and resid 1012 through 1025 Processing helix chain 'W' and resid 1032 through 1036 Processing helix chain 'W' and resid 1046 through 1089 removed outlier: 3.515A pdb=" N GLU W1073 " --> pdb=" O LYS W1069 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS W1088 " --> pdb=" O ALA W1084 " (cutoff:3.500A) Processing helix chain 'W' and resid 1104 through 1112 Processing helix chain 'W' and resid 1131 through 1148 Processing helix chain 'W' and resid 1155 through 1157 No H-bonds generated for 'chain 'W' and resid 1155 through 1157' Processing helix chain 'W' and resid 1177 through 1189 removed outlier: 3.690A pdb=" N LEU W1184 " --> pdb=" O ASP W1180 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE W1185 " --> pdb=" O GLU W1181 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY W1186 " --> pdb=" O LYS W1182 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL W1187 " --> pdb=" O LEU W1183 " (cutoff:3.500A) Processing helix chain 'W' and resid 1195 through 1198 No H-bonds generated for 'chain 'W' and resid 1195 through 1198' Processing helix chain 'W' and resid 1207 through 1209 No H-bonds generated for 'chain 'W' and resid 1207 through 1209' Processing helix chain 'W' and resid 1250 through 1265 removed outlier: 3.612A pdb=" N ARG W1256 " --> pdb=" O HIS W1252 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'W' and resid 185 through 187 Processing sheet with id= B, first strand: chain 'W' and resid 293 through 297 Processing sheet with id= C, first strand: chain 'W' and resid 397 through 399 removed outlier: 4.369A pdb=" N GLY W 397 " --> pdb=" O ARG W 537 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU W 539 " --> pdb=" O GLY W 397 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL W 512 " --> pdb=" O MET W 538 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE W 429 " --> pdb=" O ALA W 511 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASP W 513 " --> pdb=" O ILE W 429 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL W 431 " --> pdb=" O ASP W 513 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU W 488 " --> pdb=" O HIS W 428 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR W 490 " --> pdb=" O ILE W 430 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'W' and resid 612 through 616 removed outlier: 3.560A pdb=" N PHE W 767 " --> pdb=" O VAL W 714 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE W 716 " --> pdb=" O PHE W 767 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'W' and resid 179 through 182 removed outlier: 6.828A pdb=" N LYS W 216 " --> pdb=" O ASP W 180 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'W' and resid 287 through 290 removed outlier: 6.789A pdb=" N LYS W 310 " --> pdb=" O GLU W 288 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 409 hydrogen bonds 806 hydrogen bond angles 0 basepair planarities 161 basepair parallelities 249 stacking parallelities Total time for adding SS restraints: 12.76 Time building geometry restraints manager: 9.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4454 1.33 - 1.45: 5619 1.45 - 1.57: 9913 1.57 - 1.69: 648 1.69 - 1.81: 71 Bond restraints: 20705 Sorted by residual: bond pdb=" BE BEF W1502 " pdb=" F2 BEF W1502 " ideal model delta sigma weight residual 1.476 1.567 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" BE BEF W1502 " pdb=" F1 BEF W1502 " ideal model delta sigma weight residual 1.476 1.555 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" BE BEF W1502 " pdb=" F3 BEF W1502 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" CA PRO D 100 " pdb=" C PRO D 100 " ideal model delta sigma weight residual 1.520 1.554 -0.035 1.42e-02 4.96e+03 5.94e+00 bond pdb=" CA LEU H 99 " pdb=" C LEU H 99 " ideal model delta sigma weight residual 1.523 1.547 -0.024 1.06e-02 8.90e+03 5.32e+00 ... (remaining 20700 not shown) Histogram of bond angle deviations from ideal: 97.90 - 105.53: 1609 105.53 - 113.16: 11708 113.16 - 120.79: 9977 120.79 - 128.43: 5681 128.43 - 136.06: 363 Bond angle restraints: 29338 Sorted by residual: angle pdb=" C LEU D 99 " pdb=" N PRO D 100 " pdb=" CA PRO D 100 " ideal model delta sigma weight residual 119.84 127.89 -8.05 1.25e+00 6.40e-01 4.15e+01 angle pdb=" N VAL D 45 " pdb=" CA VAL D 45 " pdb=" C VAL D 45 " ideal model delta sigma weight residual 113.71 109.63 4.08 9.50e-01 1.11e+00 1.84e+01 angle pdb=" F1 BEF W1502 " pdb=" BE BEF W1502 " pdb=" F3 BEF W1502 " ideal model delta sigma weight residual 120.12 108.32 11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" N PRO D 100 " pdb=" CA PRO D 100 " pdb=" C PRO D 100 " ideal model delta sigma weight residual 112.47 120.37 -7.90 2.06e+00 2.36e-01 1.47e+01 angle pdb=" N LEU D 99 " pdb=" CA LEU D 99 " pdb=" C LEU D 99 " ideal model delta sigma weight residual 110.24 114.74 -4.50 1.46e+00 4.69e-01 9.51e+00 ... (remaining 29333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 10356 36.00 - 72.00: 1298 72.00 - 107.99: 18 107.99 - 143.99: 2 143.99 - 179.99: 3 Dihedral angle restraints: 11677 sinusoidal: 6978 harmonic: 4699 Sorted by residual: dihedral pdb=" O1B ADP W1501 " pdb=" O3A ADP W1501 " pdb=" PB ADP W1501 " pdb=" PA ADP W1501 " ideal model delta sinusoidal sigma weight residual 300.00 120.84 179.16 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP W1501 " pdb=" O5' ADP W1501 " pdb=" PA ADP W1501 " pdb=" O2A ADP W1501 " ideal model delta sinusoidal sigma weight residual -60.00 100.81 -160.80 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O2A ADP W1501 " pdb=" O3A ADP W1501 " pdb=" PA ADP W1501 " pdb=" PB ADP W1501 " ideal model delta sinusoidal sigma weight residual -60.00 52.86 -112.86 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 11674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2643 0.036 - 0.072: 521 0.072 - 0.107: 103 0.107 - 0.143: 22 0.143 - 0.179: 1 Chirality restraints: 3290 Sorted by residual: chirality pdb=" CA PRO D 100 " pdb=" N PRO D 100 " pdb=" C PRO D 100 " pdb=" CB PRO D 100 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA PRO H 100 " pdb=" N PRO H 100 " pdb=" C PRO H 100 " pdb=" CB PRO H 100 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA ILE W 290 " pdb=" N ILE W 290 " pdb=" C ILE W 290 " pdb=" CB ILE W 290 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 ... (remaining 3287 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU H 98 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.74e+00 pdb=" C LEU H 98 " 0.041 2.00e-02 2.50e+03 pdb=" O LEU H 98 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU H 99 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 98 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C LEU D 98 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU D 98 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU D 99 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 99 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C LEU H 99 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU H 99 " -0.011 2.00e-02 2.50e+03 pdb=" N PRO H 100 " -0.010 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1248 2.74 - 3.28: 18810 3.28 - 3.82: 35312 3.82 - 4.36: 41622 4.36 - 4.90: 62002 Nonbonded interactions: 158994 Sorted by model distance: nonbonded pdb=" OP2 DG J 23 " pdb=" NZ LYS W 519 " model vdw 2.194 2.520 nonbonded pdb=" O ASN W1145 " pdb=" OG SER W1149 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR D 29 " pdb=" OP1 DT I 30 " model vdw 2.278 2.440 nonbonded pdb=" OP1 DT I -16 " pdb=" NZ LYS W 497 " model vdw 2.288 2.520 nonbonded pdb=" O LEU W 655 " pdb=" OG SER W 659 " model vdw 2.309 2.440 ... (remaining 158989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.690 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: 0.020 Extract box with map and model: 3.740 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 59.980 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1302 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 0.091 20705 Z= 0.144 Angle : 0.475 11.802 29338 Z= 0.293 Chirality : 0.032 0.179 3290 Planarity : 0.003 0.028 2604 Dihedral : 22.569 179.989 8633 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.06 % Favored : 90.81 % Rotamer: Outliers : 0.36 % Allowed : 3.43 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.25 (0.16), residues: 1578 helix: -2.52 (0.12), residues: 885 sheet: -2.20 (0.56), residues: 79 loop : -3.20 (0.21), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP W 311 HIS 0.002 0.000 HIS W 285 PHE 0.007 0.001 PHE W 379 TYR 0.008 0.001 TYR A 99 ARG 0.002 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 245 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER W 635 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.2735 (mt) cc_final: 0.1340 (mt) REVERT: C 68 ASN cc_start: 0.8812 (m-40) cc_final: 0.8425 (m110) REVERT: D 60 ASN cc_start: 0.4534 (t0) cc_final: 0.3383 (m110) REVERT: E 81 ASP cc_start: 0.5207 (t0) cc_final: 0.4606 (m-30) REVERT: W 538 MET cc_start: 0.3072 (tpp) cc_final: 0.1786 (mmm) outliers start: 5 outliers final: 0 residues processed: 249 average time/residue: 0.4299 time to fit residues: 147.0972 Evaluate side-chains 113 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 31 HIS ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 185 HIS W 210 ASN W 285 HIS ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 428 HIS W 530 ASN W 622 GLN W 667 ASN ** W 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1145 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3096 moved from start: 0.8632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 20705 Z= 0.485 Angle : 1.150 15.114 29338 Z= 0.617 Chirality : 0.057 0.312 3290 Planarity : 0.011 0.136 2604 Dihedral : 29.456 178.742 5335 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 35.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.72 % Favored : 93.22 % Rotamer: Outliers : 0.93 % Allowed : 5.14 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.18), residues: 1578 helix: -1.70 (0.15), residues: 864 sheet: -1.58 (0.61), residues: 69 loop : -2.86 (0.21), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP W 417 HIS 0.016 0.003 HIS W 428 PHE 0.037 0.004 PHE C 25 TYR 0.053 0.004 TYR A 99 ARG 0.028 0.002 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.5892 (mt) cc_final: 0.5474 (mt) REVERT: B 96 THR cc_start: 0.7143 (OUTLIER) cc_final: 0.6472 (m) REVERT: C 36 LYS cc_start: 0.7378 (mppt) cc_final: 0.6613 (tppt) REVERT: D 59 MET cc_start: 0.4678 (tpt) cc_final: 0.3750 (ttt) REVERT: D 103 LEU cc_start: 0.5974 (mt) cc_final: 0.5447 (mm) REVERT: F 55 ARG cc_start: 0.4678 (mtt90) cc_final: 0.4278 (ptp-110) REVERT: G 43 VAL cc_start: 0.6174 (m) cc_final: 0.5350 (p) REVERT: W 244 ASN cc_start: 0.6268 (p0) cc_final: 0.4766 (p0) REVERT: W 387 MET cc_start: 0.6951 (mtp) cc_final: 0.6202 (mtp) REVERT: W 424 GLN cc_start: 0.5931 (mm110) cc_final: 0.4866 (tp40) REVERT: W 429 ILE cc_start: 0.4276 (tt) cc_final: 0.3727 (tt) REVERT: W 652 MET cc_start: 0.0101 (ptt) cc_final: -0.0123 (pmm) REVERT: W 681 MET cc_start: 0.6075 (tpt) cc_final: 0.5402 (tmm) outliers start: 13 outliers final: 3 residues processed: 203 average time/residue: 0.3991 time to fit residues: 115.8091 Evaluate side-chains 124 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 184 optimal weight: 0.1980 chunk 152 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN G 31 HIS G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN W 185 HIS W 205 ASN W 337 HIS ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 667 ASN W 712 HIS W 719 GLN ** W 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1145 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3072 moved from start: 0.9478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20705 Z= 0.217 Angle : 0.644 9.358 29338 Z= 0.360 Chirality : 0.038 0.159 3290 Planarity : 0.005 0.086 2604 Dihedral : 28.876 175.546 5335 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 0.21 % Allowed : 3.00 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.11 (0.19), residues: 1578 helix: -0.45 (0.16), residues: 891 sheet: -1.48 (0.62), residues: 69 loop : -2.80 (0.21), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP W 417 HIS 0.007 0.001 HIS W 285 PHE 0.017 0.002 PHE E 104 TYR 0.019 0.002 TYR A 99 ARG 0.014 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 LEU cc_start: 0.5989 (mm) cc_final: 0.5699 (pp) REVERT: D 59 MET cc_start: 0.5798 (tpt) cc_final: 0.5386 (tpt) REVERT: D 105 LYS cc_start: 0.8255 (mmpt) cc_final: 0.7860 (mmmt) REVERT: W 387 MET cc_start: 0.6741 (mtp) cc_final: 0.6231 (mtp) REVERT: W 424 GLN cc_start: 0.4355 (mm110) cc_final: 0.3698 (tp-100) REVERT: W 815 MET cc_start: 0.2208 (tmm) cc_final: 0.1720 (tmm) outliers start: 3 outliers final: 0 residues processed: 162 average time/residue: 0.3836 time to fit residues: 89.7417 Evaluate side-chains 112 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 171 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 93 GLN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS W 177 HIS W 185 HIS W 205 ASN ** W 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 285 HIS W 396 ASN W 410 GLN W 530 ASN ** W 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 667 ASN ** W 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1169 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4545 moved from start: 1.7071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.200 20705 Z= 0.580 Angle : 1.209 19.697 29338 Z= 0.659 Chirality : 0.060 0.333 3290 Planarity : 0.012 0.167 2604 Dihedral : 30.150 174.866 5335 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 46.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.38 % Favored : 90.43 % Rotamer: Outliers : 0.79 % Allowed : 6.57 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.18), residues: 1578 helix: -1.84 (0.15), residues: 849 sheet: -1.44 (0.63), residues: 60 loop : -3.08 (0.20), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.005 TRP W 507 HIS 0.026 0.004 HIS W 428 PHE 0.047 0.004 PHE E 104 TYR 0.050 0.005 TYR W 582 ARG 0.047 0.002 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 231 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7495 (tpt) cc_final: 0.7054 (tpp) REVERT: A 107 THR cc_start: 0.6851 (m) cc_final: 0.6579 (m) REVERT: A 120 MET cc_start: 0.4322 (mmt) cc_final: 0.4060 (mmt) REVERT: C 56 GLU cc_start: 0.7842 (tt0) cc_final: 0.7431 (tt0) REVERT: C 57 TYR cc_start: 0.6310 (t80) cc_final: 0.5957 (t80) REVERT: C 74 LYS cc_start: 0.8407 (mtmm) cc_final: 0.8123 (mtmm) REVERT: D 56 MET cc_start: 0.9226 (tmm) cc_final: 0.8640 (tmm) REVERT: D 59 MET cc_start: 0.8796 (tpt) cc_final: 0.8230 (tpp) REVERT: D 103 LEU cc_start: 0.7244 (mt) cc_final: 0.6917 (mt) REVERT: D 105 LYS cc_start: 0.8526 (mmpt) cc_final: 0.8252 (tppt) REVERT: E 112 ILE cc_start: 0.9030 (mt) cc_final: 0.8771 (mt) REVERT: E 134 ARG cc_start: 0.5501 (tpt-90) cc_final: 0.4752 (tpp-160) REVERT: F 44 LYS cc_start: 0.4535 (mtpt) cc_final: 0.3291 (mmmt) REVERT: H 103 LEU cc_start: 0.7503 (mt) cc_final: 0.6901 (mt) REVERT: W 243 ASP cc_start: 0.7193 (m-30) cc_final: 0.6989 (m-30) REVERT: W 387 MET cc_start: 0.6484 (mtp) cc_final: 0.6006 (mtp) REVERT: W 437 MET cc_start: 0.3821 (ttp) cc_final: 0.3600 (ttp) REVERT: W 525 LEU cc_start: 0.7188 (pp) cc_final: 0.6881 (pp) REVERT: W 802 MET cc_start: 0.4023 (tpp) cc_final: 0.2981 (tpp) outliers start: 11 outliers final: 5 residues processed: 242 average time/residue: 0.3594 time to fit residues: 126.8428 Evaluate side-chains 161 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 156 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 125 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 81 ASN E 39 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 185 HIS W 285 HIS W 591 GLN W 667 ASN ** W 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4379 moved from start: 1.7488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20705 Z= 0.233 Angle : 0.720 9.947 29338 Z= 0.406 Chirality : 0.042 0.179 3290 Planarity : 0.006 0.105 2604 Dihedral : 29.312 170.899 5335 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.93 % Rotamer: Outliers : 0.07 % Allowed : 2.64 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.23 (0.20), residues: 1578 helix: -0.71 (0.16), residues: 884 sheet: -1.03 (0.76), residues: 55 loop : -2.61 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP W 386 HIS 0.006 0.002 HIS D 106 PHE 0.030 0.002 PHE W 414 TYR 0.021 0.002 TYR D 34 ARG 0.019 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.3781 (mm-40) cc_final: 0.3515 (mm-40) REVERT: B 29 ILE cc_start: 0.7983 (mp) cc_final: 0.7612 (mm) REVERT: C 56 GLU cc_start: 0.7356 (tt0) cc_final: 0.7138 (tt0) REVERT: C 57 TYR cc_start: 0.6022 (t80) cc_final: 0.5654 (t80) REVERT: C 74 LYS cc_start: 0.8434 (mtmm) cc_final: 0.8067 (mtmm) REVERT: C 94 ASN cc_start: 0.8167 (t0) cc_final: 0.7582 (t0) REVERT: D 59 MET cc_start: 0.8889 (tpt) cc_final: 0.8270 (tpp) REVERT: D 105 LYS cc_start: 0.8366 (mmpt) cc_final: 0.8148 (tppt) REVERT: D 117 LYS cc_start: 0.8071 (tptt) cc_final: 0.7535 (tptt) REVERT: F 44 LYS cc_start: 0.4323 (mtpt) cc_final: 0.3658 (tppt) REVERT: F 70 VAL cc_start: 0.7494 (t) cc_final: 0.6861 (t) REVERT: F 100 PHE cc_start: 0.6946 (t80) cc_final: 0.6326 (t80) REVERT: H 103 LEU cc_start: 0.7201 (mt) cc_final: 0.6737 (mt) REVERT: W 452 ASN cc_start: 0.2996 (p0) cc_final: 0.2468 (p0) REVERT: W 802 MET cc_start: 0.4255 (tpp) cc_final: 0.3405 (tpp) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.3658 time to fit residues: 120.9694 Evaluate side-chains 167 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.3980 chunk 163 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 106 optimal weight: 0.0040 chunk 44 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 150 optimal weight: 0.0970 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 285 HIS W 396 ASN W 424 GLN ** W 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 530 ASN W 667 ASN ** W 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 806 HIS W 810 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4261 moved from start: 1.7570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20705 Z= 0.180 Angle : 0.625 7.190 29338 Z= 0.354 Chirality : 0.039 0.184 3290 Planarity : 0.005 0.072 2604 Dihedral : 28.865 175.329 5335 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.80 % Rotamer: Outliers : 0.14 % Allowed : 0.93 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.58 (0.20), residues: 1578 helix: -0.09 (0.17), residues: 899 sheet: -1.04 (0.75), residues: 54 loop : -2.48 (0.22), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP W 386 HIS 0.008 0.001 HIS H 106 PHE 0.022 0.002 PHE W 414 TYR 0.018 0.001 TYR A 99 ARG 0.010 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 231 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8085 (tpp80) cc_final: 0.7586 (tpp80) REVERT: C 74 LYS cc_start: 0.8342 (mtmm) cc_final: 0.7954 (mtmm) REVERT: C 94 ASN cc_start: 0.8453 (t0) cc_final: 0.7922 (m110) REVERT: D 48 ASP cc_start: 0.7015 (p0) cc_final: 0.6555 (t0) REVERT: D 59 MET cc_start: 0.8918 (tpt) cc_final: 0.8308 (tpp) REVERT: D 102 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7388 (tm-30) REVERT: D 105 LYS cc_start: 0.8752 (mmpt) cc_final: 0.8508 (tppt) REVERT: E 90 MET cc_start: 0.6942 (ptt) cc_final: 0.6437 (ptm) REVERT: F 44 LYS cc_start: 0.4484 (mtpt) cc_final: 0.3464 (mmmt) REVERT: F 70 VAL cc_start: 0.7449 (t) cc_final: 0.7162 (t) REVERT: F 100 PHE cc_start: 0.6467 (t80) cc_final: 0.6106 (t80) REVERT: H 112 THR cc_start: 0.8801 (p) cc_final: 0.8422 (t) REVERT: W 437 MET cc_start: 0.3583 (ttp) cc_final: 0.3135 (ttp) REVERT: W 617 GLU cc_start: 0.5954 (mm-30) cc_final: 0.5589 (mm-30) outliers start: 2 outliers final: 1 residues processed: 233 average time/residue: 0.3527 time to fit residues: 120.0201 Evaluate side-chains 168 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 181 optimal weight: 8.9990 chunk 113 optimal weight: 0.0980 chunk 110 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 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 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 68 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 285 HIS W 343 ASN ** W 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4788 moved from start: 1.9821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20705 Z= 0.293 Angle : 0.778 9.854 29338 Z= 0.432 Chirality : 0.043 0.242 3290 Planarity : 0.009 0.157 2604 Dihedral : 29.050 176.632 5335 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 28.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.84 % Favored : 93.09 % Rotamer: Outliers : 0.14 % Allowed : 2.43 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.84 (0.20), residues: 1578 helix: -0.38 (0.16), residues: 887 sheet: -1.04 (0.71), residues: 54 loop : -2.44 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP W 417 HIS 0.022 0.002 HIS G 31 PHE 0.040 0.003 PHE G 25 TYR 0.046 0.003 TYR H 37 ARG 0.037 0.001 ARG G 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 236 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7415 (mp0) REVERT: A 90 MET cc_start: 0.7636 (tpt) cc_final: 0.7195 (tpp) REVERT: A 100 LEU cc_start: 0.9180 (mt) cc_final: 0.8972 (mt) REVERT: B 95 ARG cc_start: 0.8258 (tpp80) cc_final: 0.7843 (tpp80) REVERT: C 36 LYS cc_start: 0.8289 (ptpt) cc_final: 0.7968 (tptp) REVERT: C 56 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8346 (mt-10) REVERT: C 61 GLU cc_start: 0.8295 (pt0) cc_final: 0.7440 (pt0) REVERT: C 74 LYS cc_start: 0.8769 (mtmm) cc_final: 0.8519 (mtmm) REVERT: D 59 MET cc_start: 0.8998 (tpt) cc_final: 0.8535 (tpp) REVERT: D 73 GLU cc_start: 0.8716 (mp0) cc_final: 0.8476 (tp30) REVERT: D 102 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7449 (tm-30) REVERT: D 105 LYS cc_start: 0.8655 (mmpt) cc_final: 0.8406 (tppt) REVERT: D 109 SER cc_start: 0.8739 (m) cc_final: 0.8281 (p) REVERT: E 90 MET cc_start: 0.7894 (ptt) cc_final: 0.7495 (ptm) REVERT: F 44 LYS cc_start: 0.6724 (mtpt) cc_final: 0.6480 (mtpt) REVERT: G 16 THR cc_start: 0.6231 (m) cc_final: 0.6005 (m) REVERT: W 437 MET cc_start: 0.3865 (ttp) cc_final: 0.3638 (ttp) REVERT: W 718 SER cc_start: 0.3409 (m) cc_final: 0.2957 (p) REVERT: W 802 MET cc_start: 0.4692 (tpp) cc_final: 0.4459 (tpt) REVERT: W 1057 MET cc_start: 0.2664 (mmm) cc_final: 0.2289 (mmm) REVERT: W 1123 LYS cc_start: -0.0970 (mmtt) cc_final: -0.1952 (ptmm) REVERT: W 1144 LYS cc_start: 0.2753 (mmtt) cc_final: 0.2209 (pttp) outliers start: 2 outliers final: 0 residues processed: 238 average time/residue: 0.3418 time to fit residues: 120.8957 Evaluate side-chains 172 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 108 optimal weight: 0.0030 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 142 optimal weight: 0.5980 chunk 164 optimal weight: 0.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 113 HIS B 93 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS W 285 HIS W 424 GLN ** W 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4616 moved from start: 1.9967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20705 Z= 0.177 Angle : 0.636 9.580 29338 Z= 0.357 Chirality : 0.039 0.174 3290 Planarity : 0.005 0.077 2604 Dihedral : 28.717 174.490 5335 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.24 (0.21), residues: 1578 helix: 0.17 (0.17), residues: 901 sheet: -0.58 (0.68), residues: 61 loop : -2.36 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP W 386 HIS 0.011 0.001 HIS A 113 PHE 0.026 0.002 PHE W 414 TYR 0.027 0.002 TYR C 39 ARG 0.012 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.6739 (tp30) cc_final: 0.6003 (tp30) REVERT: A 93 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6757 (mm110) REVERT: A 100 LEU cc_start: 0.9037 (mt) cc_final: 0.8620 (mt) REVERT: C 33 LEU cc_start: 0.8756 (mp) cc_final: 0.8451 (mt) REVERT: C 36 LYS cc_start: 0.8618 (ptpt) cc_final: 0.8003 (tptp) REVERT: C 56 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8146 (mt-10) REVERT: C 102 ILE cc_start: 0.6689 (mm) cc_final: 0.6405 (mt) REVERT: D 59 MET cc_start: 0.8937 (tpt) cc_final: 0.8642 (mmp) REVERT: D 103 LEU cc_start: 0.7338 (mp) cc_final: 0.6917 (mt) REVERT: E 90 MET cc_start: 0.7709 (ptt) cc_final: 0.7175 (ptm) REVERT: E 109 LEU cc_start: 0.7605 (mt) cc_final: 0.7214 (mt) REVERT: E 120 MET cc_start: 0.9097 (tpt) cc_final: 0.8838 (tpp) REVERT: E 122 LYS cc_start: 0.8662 (pttt) cc_final: 0.6842 (pttm) REVERT: F 44 LYS cc_start: 0.6494 (mtpt) cc_final: 0.5589 (mttt) REVERT: F 60 VAL cc_start: 0.8824 (t) cc_final: 0.8547 (t) REVERT: F 63 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7688 (mt-10) REVERT: F 84 MET cc_start: 0.1600 (mmp) cc_final: 0.0535 (ppp) REVERT: F 100 PHE cc_start: 0.6789 (t80) cc_final: 0.6130 (t80) REVERT: G 88 ARG cc_start: 0.7191 (mmt180) cc_final: 0.6384 (mmp-170) REVERT: G 102 ILE cc_start: 0.7027 (tp) cc_final: 0.6654 (tt) REVERT: W 437 MET cc_start: 0.2988 (ttp) cc_final: 0.2506 (ttp) REVERT: W 455 CYS cc_start: 0.3017 (p) cc_final: 0.2681 (p) REVERT: W 1123 LYS cc_start: -0.1202 (mmtt) cc_final: -0.2081 (ptmm) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.3612 time to fit residues: 133.4725 Evaluate side-chains 175 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 40.0000 chunk 158 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 113 HIS ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 185 HIS ** W 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5591 moved from start: 2.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.450 20705 Z= 0.577 Angle : 1.123 15.170 29338 Z= 0.611 Chirality : 0.057 0.617 3290 Planarity : 0.010 0.140 2604 Dihedral : 29.818 176.135 5335 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 46.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.95 % Favored : 89.92 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.84 (0.19), residues: 1578 helix: -1.28 (0.16), residues: 890 sheet: -1.26 (0.63), residues: 68 loop : -2.78 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.005 TRP W 417 HIS 0.019 0.003 HIS F 75 PHE 0.040 0.005 PHE W 414 TYR 0.054 0.005 TYR W 582 ARG 0.048 0.002 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8895 (mt) cc_final: 0.8602 (mm) REVERT: A 110 CYS cc_start: 0.9005 (m) cc_final: 0.7585 (t) REVERT: A 120 MET cc_start: 0.7138 (mpp) cc_final: 0.6760 (mpp) REVERT: B 26 ILE cc_start: 0.7473 (tp) cc_final: 0.7196 (tp) REVERT: B 51 TYR cc_start: 0.6365 (p90) cc_final: 0.5986 (p90) REVERT: B 52 GLU cc_start: 0.8730 (tp30) cc_final: 0.8404 (pm20) REVERT: B 58 LEU cc_start: 0.9130 (tp) cc_final: 0.8816 (tp) REVERT: B 84 MET cc_start: 0.8884 (mmp) cc_final: 0.8362 (mmm) REVERT: C 36 LYS cc_start: 0.8608 (ptpt) cc_final: 0.8322 (tptp) REVERT: C 50 TYR cc_start: 0.7967 (t80) cc_final: 0.7707 (t80) REVERT: D 92 GLN cc_start: 0.8811 (tt0) cc_final: 0.8393 (mt0) REVERT: D 113 LYS cc_start: 0.9537 (pptt) cc_final: 0.9262 (pptt) REVERT: E 90 MET cc_start: 0.8326 (ptt) cc_final: 0.8112 (mpp) REVERT: E 106 ASP cc_start: 0.8596 (t70) cc_final: 0.8113 (m-30) REVERT: E 131 ARG cc_start: 0.8021 (ptm160) cc_final: 0.7804 (ttp-170) REVERT: F 84 MET cc_start: 0.5374 (mmp) cc_final: 0.4507 (ppp) REVERT: F 100 PHE cc_start: 0.7656 (t80) cc_final: 0.6576 (t80) REVERT: G 30 VAL cc_start: 0.8381 (t) cc_final: 0.8147 (t) REVERT: G 32 ARG cc_start: 0.7761 (tpm170) cc_final: 0.7529 (mtm180) REVERT: G 81 ARG cc_start: 0.6283 (tpt170) cc_final: 0.6043 (tpp-160) REVERT: H 56 MET cc_start: 0.8884 (mmp) cc_final: 0.8429 (mmp) REVERT: W 254 GLN cc_start: 0.6255 (mp10) cc_final: 0.5465 (mp10) REVERT: W 445 GLU cc_start: 0.6378 (tt0) cc_final: 0.6049 (tm-30) REVERT: W 539 LEU cc_start: 0.6206 (tp) cc_final: 0.5479 (tt) REVERT: W 718 SER cc_start: 0.5819 (m) cc_final: 0.5493 (p) REVERT: W 1007 MET cc_start: 0.3458 (tmm) cc_final: 0.3040 (tmm) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.3475 time to fit residues: 134.9003 Evaluate side-chains 190 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.1980 chunk 84 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN W 185 HIS W 222 HIS ** W 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 2.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 20705 Z= 0.334 Angle : 0.829 13.475 29338 Z= 0.458 Chirality : 0.045 0.246 3290 Planarity : 0.008 0.123 2604 Dihedral : 29.451 161.227 5335 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 27.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.59 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.21 (0.20), residues: 1578 helix: -0.69 (0.16), residues: 905 sheet: -0.82 (0.63), residues: 64 loop : -2.69 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP W 507 HIS 0.011 0.002 HIS A 113 PHE 0.034 0.003 PHE C 25 TYR 0.082 0.004 TYR B 98 ARG 0.025 0.001 ARG B 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9097 (mt) cc_final: 0.8852 (mm) REVERT: A 51 ILE cc_start: 0.8553 (mt) cc_final: 0.8279 (mt) REVERT: A 63 ARG cc_start: 0.7471 (mpp-170) cc_final: 0.7230 (mmt180) REVERT: A 106 ASP cc_start: 0.8963 (m-30) cc_final: 0.8330 (t0) REVERT: A 110 CYS cc_start: 0.9324 (m) cc_final: 0.7780 (t) REVERT: A 115 LYS cc_start: 0.8697 (mmmt) cc_final: 0.8223 (mttt) REVERT: A 120 MET cc_start: 0.7074 (mpp) cc_final: 0.6670 (mpp) REVERT: B 26 ILE cc_start: 0.8350 (tp) cc_final: 0.8081 (tp) REVERT: B 52 GLU cc_start: 0.8750 (tp30) cc_final: 0.7835 (tp30) REVERT: B 84 MET cc_start: 0.8855 (mmp) cc_final: 0.8561 (mmm) REVERT: C 33 LEU cc_start: 0.9019 (mp) cc_final: 0.8644 (mt) REVERT: C 56 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8525 (mm-30) REVERT: E 94 GLU cc_start: 0.8988 (pt0) cc_final: 0.8535 (mt-10) REVERT: E 104 PHE cc_start: 0.7962 (t80) cc_final: 0.7698 (t80) REVERT: F 53 GLU cc_start: 0.8364 (pt0) cc_final: 0.8155 (pt0) REVERT: F 65 VAL cc_start: 0.9172 (t) cc_final: 0.8922 (p) REVERT: F 100 PHE cc_start: 0.6999 (t80) cc_final: 0.5662 (t80) REVERT: G 32 ARG cc_start: 0.7634 (tpm170) cc_final: 0.7338 (mtm110) REVERT: H 97 LEU cc_start: 0.9276 (mt) cc_final: 0.9022 (tt) REVERT: W 451 LEU cc_start: 0.6315 (mt) cc_final: 0.5844 (mt) REVERT: W 472 TYR cc_start: 0.3587 (t80) cc_final: 0.3080 (m-80) REVERT: W 473 THR cc_start: 0.7324 (p) cc_final: 0.6333 (p) REVERT: W 716 ILE cc_start: 0.7558 (pt) cc_final: 0.6753 (pt) REVERT: W 1056 MET cc_start: 0.3216 (ttp) cc_final: 0.2946 (ttm) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.3388 time to fit residues: 130.2324 Evaluate side-chains 193 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 0.0770 chunk 62 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** W 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 530 ASN W 779 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.075080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.057298 restraints weight = 173925.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.058655 restraints weight = 109073.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.059603 restraints weight = 75769.303| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 2.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20705 Z= 0.197 Angle : 0.698 8.707 29338 Z= 0.389 Chirality : 0.041 0.222 3290 Planarity : 0.005 0.085 2604 Dihedral : 29.060 163.898 5335 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.83 % Favored : 94.11 % Rotamer: Outliers : 0.07 % Allowed : 0.21 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.57 (0.20), residues: 1578 helix: -0.21 (0.17), residues: 904 sheet: -0.67 (0.67), residues: 58 loop : -2.32 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP W 507 HIS 0.009 0.001 HIS F 75 PHE 0.050 0.002 PHE C 25 TYR 0.042 0.002 TYR B 98 ARG 0.011 0.001 ARG B 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3659.02 seconds wall clock time: 67 minutes 35.86 seconds (4055.86 seconds total)