Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 07:19:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/04_2023/5o9g_3765_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/04_2023/5o9g_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_3765/04_2023/5o9g_3765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/04_2023/5o9g_3765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/04_2023/5o9g_3765_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/04_2023/5o9g_3765_neut_updated.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 10.08, per 1000 atoms: 0.51 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: 9.35 Conformation dependent library (CDL) restraints added in 2.1 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: 7.72 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: 12.60 Time building geometry restraints manager: 9.97 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: 10076 36.00 - 72.00: 1284 72.00 - 107.99: 18 107.99 - 143.99: 2 143.99 - 179.99: 3 Dihedral angle restraints: 11383 sinusoidal: 6684 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 11380 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: 0.560 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: 4.430 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 61.060 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.210 ------------------------------------------------------------------------------- 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 : 22.468 179.989 8339 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 % 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 *********************** 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 : 1.717 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 outliers start: 5 outliers final: 0 residues processed: 249 average time/residue: 0.4327 time to fit residues: 149.0388 Evaluate side-chains 110 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.719 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3341 ------------------------------------------------------------------------------- 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: 3.9990 chunk 76 optimal weight: 5.9990 chunk 147 optimal weight: 0.4980 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: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** 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 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** 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 ** W 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1065 HIS W1145 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2452 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 20705 Z= 0.335 Angle : 0.836 13.338 29338 Z= 0.451 Chirality : 0.045 0.261 3290 Planarity : 0.008 0.117 2604 Dihedral : 28.881 179.368 5041 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.94 % Favored : 94.99 % Rotamer Outliers : 0.36 % 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: -2.66 (0.19), residues: 1578 helix: -1.06 (0.15), residues: 893 sheet: -1.26 (0.65), residues: 67 loop : -2.82 (0.22), residues: 618 *********************** 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 168 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 163 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 167 average time/residue: 0.3920 time to fit residues: 95.0632 Evaluate side-chains 112 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.665 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7192 time to fit residues: 3.1768 ------------------------------------------------------------------------------- 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: 5.9990 chunk 52 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 92 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 177 HIS W 254 GLN W 396 ASN ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 591 GLN W 719 GLN W 779 ASN ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1145 ASN W1169 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3583 moved from start: 1.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.130 20705 Z= 0.423 Angle : 0.999 16.501 29338 Z= 0.543 Chirality : 0.051 0.438 3290 Planarity : 0.011 0.191 2604 Dihedral : 29.553 177.842 5041 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 33.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.35 % Favored : 92.59 % Rotamer Outliers : 0.93 % 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: -2.87 (0.19), residues: 1578 helix: -1.22 (0.16), residues: 866 sheet: -1.29 (0.60), residues: 78 loop : -2.91 (0.22), residues: 634 *********************** 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 202 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 1.665 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 outliers start: 13 outliers final: 8 residues processed: 202 average time/residue: 0.3989 time to fit residues: 115.1139 Evaluate side-chains 131 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 1.776 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3002 time to fit residues: 6.1082 ------------------------------------------------------------------------------- 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: 4.9990 chunk 128 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 162 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN H 106 HIS W 205 ASN W 337 HIS ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 530 ASN W 667 ASN W 737 ASN ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3603 moved from start: 1.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 20705 Z= 0.212 Angle : 0.653 9.640 29338 Z= 0.365 Chirality : 0.039 0.192 3290 Planarity : 0.005 0.075 2604 Dihedral : 29.132 178.091 5041 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.87 % Favored : 96.07 % Rotamer Outliers : 0.21 % 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: -1.90 (0.20), residues: 1578 helix: -0.30 (0.17), residues: 893 sheet: -1.50 (0.65), residues: 66 loop : -2.67 (0.22), residues: 619 *********************** 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 180 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 1.802 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 outliers start: 3 outliers final: 0 residues processed: 179 average time/residue: 0.3793 time to fit residues: 99.6292 Evaluate side-chains 125 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.748 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2546 ------------------------------------------------------------------------------- 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: 0.0980 chunk 103 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 155 optimal weight: 0.0980 chunk 125 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** C 110 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 205 ASN W 424 GLN W 530 ASN ** W 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 685 ASN W 712 HIS W 810 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3845 moved from start: 1.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 20705 Z= 0.221 Angle : 0.644 10.219 29338 Z= 0.361 Chirality : 0.039 0.190 3290 Planarity : 0.006 0.100 2604 Dihedral : 28.931 178.818 5041 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.96 % Favored : 93.98 % Rotamer Outliers : 0.21 % 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: -1.51 (0.20), residues: 1578 helix: 0.02 (0.17), residues: 901 sheet: -1.42 (0.65), residues: 66 loop : -2.53 (0.23), residues: 611 *********************** 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 191 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 188 time to evaluate : 1.857 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 outliers start: 3 outliers final: 0 residues processed: 190 average time/residue: 0.3745 time to fit residues: 104.7932 Evaluate side-chains 134 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.759 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5830 ------------------------------------------------------------------------------- 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: 8.9990 chunk 163 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS E 85 GLN E 108 ASN F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 205 ASN ** W 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 548 ASN ** W 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4571 moved from start: 1.8147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 20705 Z= 0.323 Angle : 0.851 16.860 29338 Z= 0.469 Chirality : 0.045 0.279 3290 Planarity : 0.009 0.133 2604 Dihedral : 29.223 178.471 5041 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 30.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.59 % Favored : 93.28 % Rotamer Outliers : 0.07 % 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: -2.17 (0.20), residues: 1578 helix: -0.73 (0.17), residues: 878 sheet: -0.56 (0.75), residues: 55 loop : -2.50 (0.23), residues: 645 *********************** 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 237 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 1.746 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 outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.3735 time to fit residues: 129.5189 Evaluate side-chains 158 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.788 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2716 ------------------------------------------------------------------------------- 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: 6.9990 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 110 optimal weight: 0.2980 chunk 83 optimal weight: 10.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 222 HIS W 343 ASN ** W 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 779 ASN ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4899 moved from start: 2.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.104 20705 Z= 0.314 Angle : 0.792 10.800 29338 Z= 0.437 Chirality : 0.044 0.375 3290 Planarity : 0.007 0.092 2604 Dihedral : 29.242 176.943 5041 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 26.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.97 % Favored : 92.97 % Rotamer Outliers : 0.07 % 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: -2.13 (0.20), residues: 1578 helix: -0.56 (0.17), residues: 883 sheet: -1.04 (0.74), residues: 56 loop : -2.68 (0.22), residues: 639 *********************** 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 259 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 1.911 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 outliers start: 1 outliers final: 1 residues processed: 259 average time/residue: 0.3746 time to fit residues: 140.4354 Evaluate side-chains 177 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 1.751 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1696 time to fit residues: 2.6402 ------------------------------------------------------------------------------- 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: 7.9990 chunk 72 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS ** W 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 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 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5336 moved from start: 2.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.130 20705 Z= 0.365 Angle : 0.905 16.268 29338 Z= 0.499 Chirality : 0.048 0.364 3290 Planarity : 0.008 0.074 2604 Dihedral : 29.576 176.802 5041 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 32.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.54 % Favored : 92.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.07 % 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: -2.42 (0.19), residues: 1578 helix: -0.81 (0.16), residues: 876 sheet: -1.18 (0.65), residues: 59 loop : -2.75 (0.22), residues: 643 *********************** 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 257 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.825 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 outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.3536 time to fit residues: 134.8958 Evaluate side-chains 177 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.761 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2828 ------------------------------------------------------------------------------- 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: 4.9990 chunk 158 optimal weight: 2.9990 chunk 168 optimal weight: 0.0270 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 51 optimal weight: 0.0370 chunk 152 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 178 optimal weight: 6.9990 overall best weight: 2.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5297 moved from start: 2.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 20705 Z= 0.243 Angle : 0.698 8.732 29338 Z= 0.392 Chirality : 0.041 0.192 3290 Planarity : 0.005 0.108 2604 Dihedral : 29.265 172.434 5041 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.27 % Favored : 93.66 % Rotamer Outliers : 0.00 % 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: -1.67 (0.20), residues: 1578 helix: -0.21 (0.17), residues: 890 sheet: -1.24 (0.58), residues: 62 loop : -2.40 (0.23), residues: 626 *********************** 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 251 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.771 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 outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3788 time to fit residues: 139.4324 Evaluate side-chains 168 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.122 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3063 ------------------------------------------------------------------------------- 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: 9.9990 chunk 84 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 285 HIS ** W 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5761 moved from start: 2.7527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.128 20705 Z= 0.388 Angle : 0.917 14.256 29338 Z= 0.508 Chirality : 0.049 0.298 3290 Planarity : 0.009 0.212 2604 Dihedral : 29.763 174.366 5041 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 33.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.00 % Favored : 90.94 % Rotamer Outliers : 0.00 % 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: -2.29 (0.20), residues: 1578 helix: -0.79 (0.16), residues: 881 sheet: -1.58 (0.64), residues: 59 loop : -2.52 (0.23), residues: 638 ********************** 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 244 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.799 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 outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.3569 time to fit residues: 127.7646 Evaluate side-chains 156 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.685 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1945 ------------------------------------------------------------------------------- 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: 0.6980 chunk 137 optimal weight: 20.0000 chunk 22 optimal weight: 0.0020 chunk 41 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 8 optimal weight: 0.0010 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 38 ASN ** W 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.073913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.055566 restraints weight = 172997.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.056924 restraints weight = 108288.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.057883 restraints weight = 75265.418| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 2.7462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 20705 Z= 0.206 Angle : 0.721 9.294 29338 Z= 0.398 Chirality : 0.042 0.220 3290 Planarity : 0.005 0.102 2604 Dihedral : 29.235 162.430 5041 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.50 % Favored : 95.44 % Rotamer Outliers : 0.00 % 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: -1.54 (0.20), residues: 1578 helix: -0.10 (0.17), residues: 904 sheet: -1.61 (0.59), residues: 69 loop : -2.34 (0.24), residues: 605 =============================================================================== Job complete usr+sys time: 3466.18 seconds wall clock time: 64 minutes 21.91 seconds (3861.91 seconds total)