Starting phenix.real_space_refine on Mon Mar 11 13:27:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmq_22261/03_2024/6xmq_22261_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmq_22261/03_2024/6xmq_22261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmq_22261/03_2024/6xmq_22261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmq_22261/03_2024/6xmq_22261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmq_22261/03_2024/6xmq_22261_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmq_22261/03_2024/6xmq_22261_updated.pdb" } resolution = 3.7 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= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 5410 2.51 5 N 1375 2.21 5 O 1536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ARG 588": "NH1" <-> "NH2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 656": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 760": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A GLU 1079": "OE1" <-> "OE2" Residue "A ARG 1086": "NH1" <-> "NH2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A GLU 1190": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8362 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8362 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'peptide': 1085, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 48, 'TRANS': 1036, None: 2} Not linked: pdbres="LYS A1211 " pdbres="ACP A1301 " Not linked: pdbres="ACP A1301 " pdbres=" MG A1302 " Chain breaks: 3 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Time building chain proxies: 5.01, per 1000 atoms: 0.60 Number of scatterers: 8362 At special positions: 0 Unit cell: (84.49, 95.2, 136.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 37 16.00 P 3 15.00 Mg 1 11.99 O 1536 8.00 N 1375 7.00 C 5410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 8 sheets defined 43.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 29 through 43 removed outlier: 3.595A pdb=" N PHE A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 56 through 76 removed outlier: 3.568A pdb=" N VAL A 59 " --> pdb=" O TRP A 56 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET A 72 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Proline residue: A 75 - end of helix Processing helix chain 'A' and resid 79 through 86 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.956A pdb=" N GLN A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 189 through 197 Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 219 through 249 removed outlier: 3.524A pdb=" N ARG A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N MET A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 397 through 423 removed outlier: 3.900A pdb=" N TYR A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 441 removed outlier: 4.536A pdb=" N LEU A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 465 removed outlier: 3.592A pdb=" N ALA A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 479 Proline residue: A 476 - end of helix Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.695A pdb=" N GLY A 530 " --> pdb=" O ILE A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 607 through 612 removed outlier: 4.152A pdb=" N GLU A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 removed outlier: 3.848A pdb=" N TYR A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 626 " --> pdb=" O ASP A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 688 removed outlier: 3.809A pdb=" N ILE A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 684 " --> pdb=" O ILE A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 711 Processing helix chain 'A' and resid 754 through 757 No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 767 through 772 Processing helix chain 'A' and resid 779 through 785 removed outlier: 3.697A pdb=" N ARG A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS A 785 " --> pdb=" O ASP A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 807 Processing helix chain 'A' and resid 818 through 826 removed outlier: 3.849A pdb=" N VAL A 821 " --> pdb=" O THR A 818 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLY A 822 " --> pdb=" O ASN A 819 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 825 " --> pdb=" O GLY A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 850 Processing helix chain 'A' and resid 973 through 1011 Processing helix chain 'A' and resid 1018 through 1035 removed outlier: 4.107A pdb=" N CYS A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1083 Processing helix chain 'A' and resid 1100 through 1120 removed outlier: 4.139A pdb=" N PHE A1117 " --> pdb=" O GLN A1113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A1118 " --> pdb=" O VAL A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1151 Processing helix chain 'A' and resid 1156 through 1162 Processing helix chain 'A' and resid 1169 through 1197 removed outlier: 4.114A pdb=" N ILE A1173 " --> pdb=" O ASP A1169 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A1179 " --> pdb=" O LEU A1175 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.801A pdb=" N TYR A 102 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER A 15 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 100 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU A 17 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N HIS A 98 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 111 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 116 through 120 Processing sheet with id= C, first strand: chain 'A' and resid 256 through 260 Processing sheet with id= D, first strand: chain 'A' and resid 277 through 280 removed outlier: 7.195A pdb=" N ASP A 292 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 467 through 469 removed outlier: 3.603A pdb=" N ALA A 832 " --> pdb=" O PHE A 964 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 829 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL A 483 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N CYS A 814 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N CYS A 485 " --> pdb=" O CYS A 814 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ARG A 692 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE A 486 " --> pdb=" O ARG A 692 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A 694 " --> pdb=" O PHE A 486 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 497 through 501 removed outlier: 3.642A pdb=" N VAL A 498 " --> pdb=" O HIS A 672 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE A 670 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 638 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE A 668 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 636 " --> pdb=" O PHE A 668 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE A 670 " --> pdb=" O ARG A 634 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ARG A 634 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 600 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 578 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER A 594 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE A 576 " --> pdb=" O SER A 594 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 733 through 735 Processing sheet with id= H, first strand: chain 'A' and resid 764 through 766 removed outlier: 6.505A pdb=" N VAL A 788 " --> pdb=" O VAL A 765 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 343 hydrogen bonds defined for protein. 954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2661 1.35 - 1.48: 2089 1.48 - 1.60: 3725 1.60 - 1.73: 4 1.73 - 1.86: 64 Bond restraints: 8543 Sorted by residual: bond pdb=" C1' ACP A1301 " pdb=" O4' ACP A1301 " ideal model delta sigma weight residual 1.390 1.615 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C1' ACP A1301 " pdb=" C2' ACP A1301 " ideal model delta sigma weight residual 1.527 1.304 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C4' ACP A1301 " pdb=" O4' ACP A1301 " ideal model delta sigma weight residual 1.428 1.301 0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C6 ACP A1301 " pdb=" N6 ACP A1301 " ideal model delta sigma weight residual 1.335 1.448 -0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" C2' ACP A1301 " pdb=" O2' ACP A1301 " ideal model delta sigma weight residual 1.401 1.490 -0.089 2.00e-02 2.50e+03 1.99e+01 ... (remaining 8538 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.28: 233 106.28 - 113.21: 4798 113.21 - 120.15: 2989 120.15 - 127.09: 3501 127.09 - 134.02: 89 Bond angle restraints: 11610 Sorted by residual: angle pdb=" O3A ACP A1301 " pdb=" PA ACP A1301 " pdb=" O5' ACP A1301 " ideal model delta sigma weight residual 93.75 107.00 -13.25 3.00e+00 1.11e-01 1.95e+01 angle pdb=" N1 ACP A1301 " pdb=" C6 ACP A1301 " pdb=" N6 ACP A1301 " ideal model delta sigma weight residual 119.32 108.84 10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C3B ACP A1301 " pdb=" PB ACP A1301 " pdb=" O3A ACP A1301 " ideal model delta sigma weight residual 98.05 108.34 -10.29 3.00e+00 1.11e-01 1.18e+01 angle pdb=" O1B ACP A1301 " pdb=" PB ACP A1301 " pdb=" O2B ACP A1301 " ideal model delta sigma weight residual 119.60 110.06 9.54 3.00e+00 1.11e-01 1.01e+01 angle pdb=" O1A ACP A1301 " pdb=" PA ACP A1301 " pdb=" O2A ACP A1301 " ideal model delta sigma weight residual 118.95 110.47 8.48 3.00e+00 1.11e-01 7.99e+00 ... (remaining 11605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.49: 4751 18.49 - 36.98: 313 36.98 - 55.46: 31 55.46 - 73.95: 13 73.95 - 92.44: 8 Dihedral angle restraints: 5116 sinusoidal: 1964 harmonic: 3152 Sorted by residual: dihedral pdb=" O1B ACP A1301 " pdb=" C3B ACP A1301 " pdb=" PB ACP A1301 " pdb=" PG ACP A1301 " ideal model delta sinusoidal sigma weight residual -52.82 39.62 -92.44 1 3.00e+01 1.11e-03 1.11e+01 dihedral pdb=" CB GLU A 420 " pdb=" CG GLU A 420 " pdb=" CD GLU A 420 " pdb=" OE1 GLU A 420 " ideal model delta sinusoidal sigma weight residual 0.00 89.81 -89.81 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 520 " pdb=" CG GLU A 520 " pdb=" CD GLU A 520 " pdb=" OE1 GLU A 520 " ideal model delta sinusoidal sigma weight residual 0.00 89.40 -89.40 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1163 0.057 - 0.114: 180 0.114 - 0.171: 18 0.171 - 0.227: 0 0.227 - 0.284: 1 Chirality restraints: 1362 Sorted by residual: chirality pdb=" C2' ACP A1301 " pdb=" C1' ACP A1301 " pdb=" C3' ACP A1301 " pdb=" O2' ACP A1301 " both_signs ideal model delta sigma weight residual False -2.75 -2.47 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ILE A 301 " pdb=" N ILE A 301 " pdb=" C ILE A 301 " pdb=" CB ILE A 301 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 289 " pdb=" N ILE A 289 " pdb=" C ILE A 289 " pdb=" CB ILE A 289 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 1359 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1039 " 0.023 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO A1040 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A1040 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1040 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 273 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A 274 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 962 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO A 963 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 963 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 963 " 0.017 5.00e-02 4.00e+02 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 18 2.31 - 2.96: 3945 2.96 - 3.60: 11725 3.60 - 4.25: 16820 4.25 - 4.90: 28791 Nonbonded interactions: 61299 Sorted by model distance: nonbonded pdb=" O3G ACP A1301 " pdb="MG MG A1302 " model vdw 1.660 2.170 nonbonded pdb=" OD2 ASP A 816 " pdb="MG MG A1302 " model vdw 2.005 2.170 nonbonded pdb=" OD2 ASP A 487 " pdb="MG MG A1302 " model vdw 2.042 2.170 nonbonded pdb=" OD2 ASP A 487 " pdb=" O3G ACP A1301 " model vdw 2.080 3.040 nonbonded pdb=" OD1 ASP A 816 " pdb="MG MG A1302 " model vdw 2.102 2.170 ... (remaining 61294 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.910 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.230 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.006 0.225 8543 Z= 0.365 Angle : 0.662 13.253 11610 Z= 0.343 Chirality : 0.042 0.284 1362 Planarity : 0.004 0.036 1460 Dihedral : 13.161 92.440 3074 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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: -1.63 (0.23), residues: 1077 helix: -0.19 (0.21), residues: 489 sheet: -1.75 (0.40), residues: 132 loop : -1.80 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 137 HIS 0.004 0.001 HIS A 706 PHE 0.016 0.002 PHE A 237 TYR 0.013 0.001 TYR A 625 ARG 0.004 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.052 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2234 time to fit residues: 21.6438 Evaluate side-chains 36 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 166 HIS A 514 HIS A 620 ASN A 776 HIS A 785 HIS A 826 GLN A 987 ASN A1065 GLN A1069 HIS A1122 GLN A1209 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8543 Z= 0.206 Angle : 0.513 7.728 11610 Z= 0.267 Chirality : 0.039 0.145 1362 Planarity : 0.004 0.034 1460 Dihedral : 6.891 83.589 1178 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.46 % Allowed : 9.90 % Favored : 88.64 % 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: -0.26 (0.25), residues: 1077 helix: 1.20 (0.24), residues: 490 sheet: -1.15 (0.45), residues: 119 loop : -1.40 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 212 HIS 0.004 0.001 HIS A 533 PHE 0.015 0.001 PHE A1016 TYR 0.010 0.001 TYR A 625 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.943 Fit side-chains REVERT: A 239 ARG cc_start: 0.9030 (mmm-85) cc_final: 0.8786 (tpt170) REVERT: A 246 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.8270 (t80) REVERT: A 807 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8522 (mtm) outliers start: 13 outliers final: 7 residues processed: 50 average time/residue: 0.1712 time to fit residues: 13.4178 Evaluate side-chains 45 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8543 Z= 0.158 Angle : 0.471 6.813 11610 Z= 0.242 Chirality : 0.038 0.137 1362 Planarity : 0.003 0.030 1460 Dihedral : 6.431 86.815 1178 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.24 % Allowed : 12.49 % Favored : 86.28 % 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: 0.35 (0.25), residues: 1077 helix: 1.87 (0.24), residues: 476 sheet: -0.86 (0.44), residues: 127 loop : -1.19 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 787 HIS 0.004 0.001 HIS A 533 PHE 0.012 0.001 PHE A 405 TYR 0.008 0.001 TYR A 625 ARG 0.002 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.973 Fit side-chains REVERT: A 239 ARG cc_start: 0.9073 (mmm-85) cc_final: 0.8811 (tpt170) REVERT: A 306 MET cc_start: 0.8823 (mmm) cc_final: 0.8491 (tpp) REVERT: A 813 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.6719 (ttt) REVERT: A 1162 MET cc_start: 0.9068 (mmm) cc_final: 0.8849 (tpt) outliers start: 11 outliers final: 4 residues processed: 47 average time/residue: 0.1672 time to fit residues: 12.5149 Evaluate side-chains 44 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 50 optimal weight: 0.0050 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 0.0970 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8543 Z= 0.171 Angle : 0.471 8.014 11610 Z= 0.239 Chirality : 0.038 0.141 1362 Planarity : 0.003 0.030 1460 Dihedral : 6.103 80.905 1178 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.24 % Allowed : 14.85 % Favored : 83.91 % 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: 0.54 (0.26), residues: 1077 helix: 2.08 (0.24), residues: 476 sheet: -0.94 (0.42), residues: 137 loop : -1.09 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 787 HIS 0.003 0.001 HIS A 533 PHE 0.011 0.001 PHE A1016 TYR 0.008 0.001 TYR A 625 ARG 0.002 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.955 Fit side-chains REVERT: A 239 ARG cc_start: 0.9066 (mmm-85) cc_final: 0.8796 (tpt170) REVERT: A 306 MET cc_start: 0.8815 (mmm) cc_final: 0.8480 (tpp) outliers start: 11 outliers final: 8 residues processed: 48 average time/residue: 0.1686 time to fit residues: 12.9031 Evaluate side-chains 46 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8543 Z= 0.162 Angle : 0.454 6.164 11610 Z= 0.231 Chirality : 0.037 0.140 1362 Planarity : 0.003 0.030 1460 Dihedral : 5.947 77.587 1178 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.91 % Allowed : 16.42 % Favored : 81.66 % 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: 0.62 (0.26), residues: 1077 helix: 2.16 (0.24), residues: 477 sheet: -0.99 (0.40), residues: 148 loop : -1.02 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 787 HIS 0.003 0.000 HIS A 533 PHE 0.010 0.001 PHE A1016 TYR 0.008 0.001 TYR A 625 ARG 0.001 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 41 time to evaluate : 1.001 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 52 average time/residue: 0.1812 time to fit residues: 14.9711 Evaluate side-chains 51 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 104 optimal weight: 0.3980 chunk 86 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8543 Z= 0.357 Angle : 0.583 6.562 11610 Z= 0.298 Chirality : 0.040 0.141 1362 Planarity : 0.004 0.036 1460 Dihedral : 6.239 82.401 1178 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.14 % Allowed : 18.22 % Favored : 79.64 % 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: 0.36 (0.26), residues: 1077 helix: 1.81 (0.24), residues: 488 sheet: -1.39 (0.42), residues: 139 loop : -0.96 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 558 HIS 0.004 0.001 HIS A 691 PHE 0.017 0.002 PHE A 246 TYR 0.015 0.001 TYR A 625 ARG 0.003 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 37 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8497 (mm) outliers start: 19 outliers final: 12 residues processed: 50 average time/residue: 0.1717 time to fit residues: 13.5950 Evaluate side-chains 49 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 36 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8543 Z= 0.192 Angle : 0.480 6.621 11610 Z= 0.246 Chirality : 0.038 0.142 1362 Planarity : 0.003 0.035 1460 Dihedral : 5.980 75.093 1178 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.02 % Allowed : 19.57 % Favored : 78.40 % 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: 0.59 (0.26), residues: 1077 helix: 2.06 (0.24), residues: 481 sheet: -1.19 (0.42), residues: 139 loop : -0.92 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 137 HIS 0.003 0.001 HIS A 533 PHE 0.011 0.001 PHE A1016 TYR 0.012 0.001 TYR A1010 ARG 0.002 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 41 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9128 (mmm160) cc_final: 0.8833 (tpt170) REVERT: A 295 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8456 (mm) outliers start: 18 outliers final: 14 residues processed: 55 average time/residue: 0.1648 time to fit residues: 14.4471 Evaluate side-chains 53 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8543 Z= 0.215 Angle : 0.490 7.983 11610 Z= 0.250 Chirality : 0.038 0.142 1362 Planarity : 0.003 0.032 1460 Dihedral : 5.895 73.762 1178 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.02 % Allowed : 19.80 % Favored : 78.18 % 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: 0.63 (0.26), residues: 1077 helix: 2.10 (0.24), residues: 480 sheet: -1.09 (0.43), residues: 139 loop : -0.92 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 787 HIS 0.003 0.001 HIS A 706 PHE 0.011 0.001 PHE A 499 TYR 0.014 0.001 TYR A1010 ARG 0.002 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 38 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9088 (mmm160) cc_final: 0.8807 (tpt170) REVERT: A 295 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8492 (mm) outliers start: 18 outliers final: 15 residues processed: 52 average time/residue: 0.1684 time to fit residues: 13.9665 Evaluate side-chains 53 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 37 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.1980 chunk 97 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8543 Z= 0.196 Angle : 0.495 11.049 11610 Z= 0.248 Chirality : 0.038 0.141 1362 Planarity : 0.003 0.034 1460 Dihedral : 5.793 71.244 1178 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.02 % Allowed : 20.13 % Favored : 77.84 % 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: 0.68 (0.26), residues: 1077 helix: 2.13 (0.24), residues: 480 sheet: -0.90 (0.44), residues: 134 loop : -0.94 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 787 HIS 0.003 0.001 HIS A 533 PHE 0.011 0.001 PHE A1016 TYR 0.017 0.001 TYR A1010 ARG 0.002 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 39 time to evaluate : 1.052 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 53 average time/residue: 0.1664 time to fit residues: 13.9912 Evaluate side-chains 53 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8543 Z= 0.152 Angle : 0.488 12.556 11610 Z= 0.242 Chirality : 0.037 0.140 1362 Planarity : 0.003 0.032 1460 Dihedral : 5.639 68.011 1178 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.46 % Allowed : 20.47 % Favored : 78.07 % 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: 0.74 (0.26), residues: 1077 helix: 2.15 (0.24), residues: 479 sheet: -0.78 (0.44), residues: 134 loop : -0.91 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 787 HIS 0.003 0.000 HIS A 533 PHE 0.011 0.001 PHE A1016 TYR 0.020 0.001 TYR A1010 ARG 0.002 0.000 ARG A 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 1.026 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 52 average time/residue: 0.1730 time to fit residues: 14.1993 Evaluate side-chains 52 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.070770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.058959 restraints weight = 30872.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.060847 restraints weight = 16576.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.062103 restraints weight = 10945.152| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8543 Z= 0.160 Angle : 0.492 12.425 11610 Z= 0.244 Chirality : 0.037 0.140 1362 Planarity : 0.003 0.033 1460 Dihedral : 5.577 68.013 1178 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.80 % Allowed : 20.25 % Favored : 77.95 % 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: 0.70 (0.26), residues: 1077 helix: 2.10 (0.24), residues: 480 sheet: -0.72 (0.44), residues: 134 loop : -0.94 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 787 HIS 0.003 0.000 HIS A 533 PHE 0.014 0.001 PHE A1016 TYR 0.010 0.001 TYR A1010 ARG 0.004 0.000 ARG A 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1481.84 seconds wall clock time: 28 minutes 7.42 seconds (1687.42 seconds total)