Starting phenix.real_space_refine on Fri Dec 8 12:15:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmt_22263/12_2023/6xmt_22263_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmt_22263/12_2023/6xmt_22263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmt_22263/12_2023/6xmt_22263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmt_22263/12_2023/6xmt_22263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmt_22263/12_2023/6xmt_22263_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmt_22263/12_2023/6xmt_22263_updated.pdb" } resolution = 3.3 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= 0.057 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 Mg 1 5.21 5 S 38 5.16 5 Be 1 3.05 5 C 5370 2.51 5 N 1374 2.21 5 O 1537 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A GLU 271": "OE1" <-> "OE2" 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 420": "OE1" <-> "OE2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A ARG 480": "NH1" <-> "NH2" 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 630": "NH1" <-> "NH2" Residue "A ARG 656": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A GLU 839": "OE1" <-> "OE2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A GLU 1160": "OE1" <-> "OE2" Residue "A PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8324 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1094, 8324 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'peptide': 1092, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 49, 'TRANS': 1042, None: 2} Not linked: pdbres="LYS A1211 " pdbres="BEF A1301 " Not linked: pdbres="BEF A1301 " pdbres=" MG A1302 " Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 164 Time building chain proxies: 5.03, per 1000 atoms: 0.60 Number of scatterers: 8324 At special positions: 0 Unit cell: (91.63, 88.06, 145.18, 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 38 16.00 Mg 1 11.99 F 3 9.00 O 1537 8.00 N 1374 7.00 C 5370 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: 3.39 Conformation dependent library (CDL) restraints added in 1.8 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 9 sheets defined 41.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 27 through 43 Proline residue: A 31 - end of helix Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 58 through 77 Proline residue: A 75 - end of helix Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 189 through 198 removed outlier: 3.929A pdb=" N VAL A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 213 Processing helix chain 'A' and resid 219 through 246 removed outlier: 3.697A pdb=" N MET A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 removed outlier: 4.409A pdb=" N ILE A 336 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 337 " --> pdb=" O ASP A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 333 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 387 Processing helix chain 'A' and resid 397 through 424 Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.627A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 464 Proline residue: A 448 - end of helix removed outlier: 4.022A pdb=" N ALA A 463 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 464 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 476 through 479 removed outlier: 3.507A pdb=" N GLY A 479 " --> pdb=" O PRO A 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 476 through 479' Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.791A 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 611 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 656 through 659 No H-bonds generated for 'chain 'A' and resid 656 through 659' Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.669A pdb=" N SER A 689 " --> pdb=" O MET A 685 " (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 771 Processing helix chain 'A' and resid 779 through 783 Processing helix chain 'A' and resid 796 through 807 Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 838 through 853 Processing helix chain 'A' and resid 973 through 1011 removed outlier: 3.667A pdb=" N CYS A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N MET A1011 " --> pdb=" O SER A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1034 Processing helix chain 'A' and resid 1056 through 1083 Processing helix chain 'A' and resid 1100 through 1118 removed outlier: 4.243A pdb=" N ILE A1108 " --> pdb=" O GLY A1104 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A1117 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1151 Processing helix chain 'A' and resid 1156 through 1161 Processing helix chain 'A' and resid 1170 through 1196 Processing sheet with id= A, first strand: chain 'A' and resid 111 through 114 removed outlier: 3.579A pdb=" N GLY A 111 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 127 through 130 removed outlier: 3.586A pdb=" N PHE A 128 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 263 through 267 removed outlier: 4.862A pdb=" N ASN A 257 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 279 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU A 277 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP A 292 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 314 through 316 removed outlier: 3.771A pdb=" N SER A 299 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN A 347 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN A 303 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA A 345 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 467 through 469 removed outlier: 6.336A pdb=" N MET A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU A 833 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY A 815 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 483 through 486 removed outlier: 6.465A pdb=" N ARG A 692 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N PHE A 486 " --> pdb=" O ARG A 692 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE A 694 " --> pdb=" O PHE A 486 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.684A pdb=" N LEU A 638 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N SER A 594 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE A 576 " --> pdb=" O SER A 594 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 742 through 744 removed outlier: 3.614A pdb=" N ASP A 722 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP A 762 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N LEU A 721 " --> pdb=" O ASP A 762 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA A 764 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N ARG A 723 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP A 787 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL A 765 " --> pdb=" O TRP A 787 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR A 789 " --> pdb=" O VAL A 765 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 498 through 501 removed outlier: 3.662A pdb=" N VAL A 498 " --> pdb=" O HIS A 672 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE A 670 " --> pdb=" O GLU A 500 " (cutoff:3.500A) 346 hydrogen bonds defined for protein. 972 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: 2.54 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2200 1.33 - 1.45: 1399 1.45 - 1.57: 4832 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 8494 Sorted by residual: bond pdb=" BE BEF A1301 " pdb=" F2 BEF A1301 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" BE BEF A1301 " pdb=" F3 BEF A1301 " ideal model delta sigma weight residual 1.476 1.545 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" BE BEF A1301 " pdb=" F1 BEF A1301 " ideal model delta sigma weight residual 1.476 1.534 -0.058 2.00e-02 2.50e+03 8.32e+00 bond pdb=" N VAL A 29 " pdb=" CA VAL A 29 " ideal model delta sigma weight residual 1.460 1.483 -0.023 1.19e-02 7.06e+03 3.79e+00 bond pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 1.524 1.548 -0.024 1.23e-02 6.61e+03 3.68e+00 ... (remaining 8489 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.85: 200 105.85 - 112.90: 4653 112.90 - 119.96: 2784 119.96 - 127.02: 3806 127.02 - 134.07: 87 Bond angle restraints: 11530 Sorted by residual: angle pdb=" N VAL A 29 " pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 110.53 117.37 -6.84 9.40e-01 1.13e+00 5.30e+01 angle pdb=" C LEU A 30 " pdb=" N PRO A 31 " pdb=" CA PRO A 31 " ideal model delta sigma weight residual 119.05 125.60 -6.55 1.11e+00 8.12e-01 3.48e+01 angle pdb=" N PRO A 34 " pdb=" CA PRO A 34 " pdb=" CB PRO A 34 " ideal model delta sigma weight residual 103.33 109.78 -6.45 1.10e+00 8.26e-01 3.44e+01 angle pdb=" F2 BEF A1301 " pdb=" BE BEF A1301 " pdb=" F3 BEF A1301 " ideal model delta sigma weight residual 119.96 107.27 12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" N VAL A 198 " pdb=" CA VAL A 198 " pdb=" C VAL A 198 " ideal model delta sigma weight residual 113.42 108.96 4.46 1.17e+00 7.31e-01 1.45e+01 ... (remaining 11525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 4658 17.44 - 34.87: 370 34.87 - 52.31: 50 52.31 - 69.74: 6 69.74 - 87.18: 4 Dihedral angle restraints: 5088 sinusoidal: 1922 harmonic: 3166 Sorted by residual: dihedral pdb=" N PRO A 34 " pdb=" C PRO A 34 " pdb=" CA PRO A 34 " pdb=" CB PRO A 34 " ideal model delta harmonic sigma weight residual 115.10 123.28 -8.18 0 2.50e+00 1.60e-01 1.07e+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 -87.18 87.18 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CA TYR A 516 " pdb=" C TYR A 516 " pdb=" N SER A 517 " pdb=" CA SER A 517 " ideal model delta harmonic sigma weight residual -180.00 -164.24 -15.76 0 5.00e+00 4.00e-02 9.94e+00 ... (remaining 5085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1104 0.052 - 0.104: 219 0.104 - 0.156: 28 0.156 - 0.208: 1 0.208 - 0.260: 1 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA PRO A 34 " pdb=" N PRO A 34 " pdb=" C PRO A 34 " pdb=" CB PRO A 34 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CG LEU A 73 " pdb=" CB LEU A 73 " pdb=" CD1 LEU A 73 " pdb=" CD2 LEU A 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CG LEU A 70 " pdb=" CB LEU A 70 " pdb=" CD1 LEU A 70 " pdb=" CD2 LEU A 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.15 2.00e-01 2.50e+01 6.01e-01 ... (remaining 1350 not shown) Planarity restraints: 1464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 74 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 75 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 29 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C VAL A 29 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 29 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 30 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 273 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO A 274 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " 0.022 5.00e-02 4.00e+02 ... (remaining 1461 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 28 2.43 - 3.05: 5232 3.05 - 3.67: 11595 3.67 - 4.28: 16456 4.28 - 4.90: 28518 Nonbonded interactions: 61829 Sorted by model distance: nonbonded pdb=" F1 BEF A1301 " pdb="MG MG A1302 " model vdw 1.814 2.120 nonbonded pdb=" OD2 ASP A 487 " pdb=" F1 BEF A1301 " model vdw 1.884 2.390 nonbonded pdb=" OD1 ASN A 987 " pdb=" NH1 ARG A1127 " model vdw 2.249 2.520 nonbonded pdb=" O THR A 489 " pdb="MG MG A1302 " model vdw 2.275 2.170 nonbonded pdb=" OG1 THR A 751 " pdb=" OE1 GLN A 778 " model vdw 2.276 2.440 ... (remaining 61824 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.810 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 26.640 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.004 0.084 8494 Z= 0.236 Angle : 0.606 12.687 11530 Z= 0.347 Chirality : 0.042 0.260 1353 Planarity : 0.004 0.041 1464 Dihedral : 12.442 87.180 3036 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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: -2.38 (0.23), residues: 1082 helix: -0.21 (0.22), residues: 490 sheet: -2.82 (0.38), residues: 131 loop : -2.73 (0.24), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1187 HIS 0.005 0.001 HIS A 672 PHE 0.014 0.001 PHE A 405 TYR 0.014 0.001 TYR A1057 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.028 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1740 time to fit residues: 15.0064 Evaluate side-chains 35 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.0050 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 129 GLN A 166 HIS A 196 HIS A1050 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8494 Z= 0.144 Angle : 0.499 8.585 11530 Z= 0.254 Chirality : 0.040 0.168 1353 Planarity : 0.004 0.038 1464 Dihedral : 4.001 15.733 1149 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.68 % Allowed : 8.42 % Favored : 90.90 % 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: -1.23 (0.25), residues: 1082 helix: 0.86 (0.24), residues: 487 sheet: -2.60 (0.38), residues: 145 loop : -2.09 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 787 HIS 0.007 0.001 HIS A 672 PHE 0.015 0.001 PHE A 226 TYR 0.012 0.001 TYR A 219 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.930 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 46 average time/residue: 0.1483 time to fit residues: 11.5951 Evaluate side-chains 41 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0870 time to fit residues: 1.6475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 10.0000 chunk 30 optimal weight: 0.0000 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 33 optimal weight: 0.0970 chunk 79 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 HIS ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8494 Z= 0.149 Angle : 0.481 7.810 11530 Z= 0.242 Chirality : 0.039 0.151 1353 Planarity : 0.003 0.037 1464 Dihedral : 3.862 14.919 1149 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.25 % Allowed : 9.67 % Favored : 89.08 % 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 (0.25), residues: 1082 helix: 1.35 (0.24), residues: 488 sheet: -2.29 (0.39), residues: 142 loop : -1.78 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 787 HIS 0.006 0.001 HIS A 672 PHE 0.017 0.001 PHE A 226 TYR 0.017 0.001 TYR A 219 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.960 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 49 average time/residue: 0.1512 time to fit residues: 12.4378 Evaluate side-chains 44 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0814 time to fit residues: 2.0821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8494 Z= 0.182 Angle : 0.499 12.136 11530 Z= 0.245 Chirality : 0.039 0.152 1353 Planarity : 0.003 0.037 1464 Dihedral : 3.856 15.310 1149 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.34 % Allowed : 12.17 % Favored : 87.49 % 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: -0.29 (0.26), residues: 1082 helix: 1.71 (0.24), residues: 481 sheet: -2.12 (0.39), residues: 145 loop : -1.64 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 787 HIS 0.007 0.001 HIS A 672 PHE 0.018 0.001 PHE A 226 TYR 0.012 0.001 TYR A 219 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 1.038 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 42 average time/residue: 0.1510 time to fit residues: 10.8359 Evaluate side-chains 41 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0915 time to fit residues: 1.8822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 0.1980 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 26 optimal weight: 0.0670 chunk 35 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8494 Z= 0.122 Angle : 0.469 10.445 11530 Z= 0.230 Chirality : 0.038 0.155 1353 Planarity : 0.003 0.036 1464 Dihedral : 3.715 15.008 1149 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.57 % Allowed : 13.20 % Favored : 86.23 % 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: 0.00 (0.26), residues: 1082 helix: 1.91 (0.25), residues: 482 sheet: -1.83 (0.40), residues: 142 loop : -1.50 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 787 HIS 0.006 0.001 HIS A 672 PHE 0.018 0.001 PHE A 226 TYR 0.010 0.001 TYR A 219 ARG 0.001 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.970 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.1604 time to fit residues: 13.3028 Evaluate side-chains 40 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0736 time to fit residues: 1.7821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 55 optimal weight: 0.0010 chunk 101 optimal weight: 4.9990 overall best weight: 2.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8494 Z= 0.409 Angle : 0.613 9.964 11530 Z= 0.307 Chirality : 0.042 0.154 1353 Planarity : 0.004 0.037 1464 Dihedral : 4.251 16.428 1149 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.14 % Allowed : 14.11 % Favored : 84.76 % 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: -0.16 (0.26), residues: 1082 helix: 1.75 (0.24), residues: 483 sheet: -1.92 (0.40), residues: 142 loop : -1.57 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 137 HIS 0.008 0.001 HIS A 672 PHE 0.023 0.002 PHE A 405 TYR 0.016 0.002 TYR A1057 ARG 0.005 0.001 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 1.157 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 47 average time/residue: 0.1644 time to fit residues: 12.6812 Evaluate side-chains 46 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0853 time to fit residues: 2.5930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A1113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8494 Z= 0.160 Angle : 0.505 9.418 11530 Z= 0.248 Chirality : 0.039 0.148 1353 Planarity : 0.003 0.035 1464 Dihedral : 3.987 15.969 1149 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.11 % Allowed : 16.15 % Favored : 83.73 % 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: 0.11 (0.26), residues: 1082 helix: 1.97 (0.25), residues: 482 sheet: -1.97 (0.41), residues: 139 loop : -1.35 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1187 HIS 0.007 0.001 HIS A 672 PHE 0.019 0.001 PHE A 226 TYR 0.008 0.001 TYR A 219 ARG 0.001 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.092 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.1663 time to fit residues: 11.2320 Evaluate side-chains 39 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 20 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 71 optimal weight: 0.0020 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8494 Z= 0.195 Angle : 0.515 9.267 11530 Z= 0.252 Chirality : 0.039 0.149 1353 Planarity : 0.003 0.035 1464 Dihedral : 3.976 15.708 1149 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.34 % Allowed : 16.27 % Favored : 83.39 % 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: 0.21 (0.26), residues: 1082 helix: 2.05 (0.25), residues: 477 sheet: -1.71 (0.43), residues: 130 loop : -1.35 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1187 HIS 0.006 0.001 HIS A 672 PHE 0.020 0.001 PHE A 226 TYR 0.013 0.001 TYR A 28 ARG 0.002 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 1.054 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 43 average time/residue: 0.1550 time to fit residues: 11.2853 Evaluate side-chains 42 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0793 time to fit residues: 1.6828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 76 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 8494 Z= 0.125 Angle : 0.494 9.095 11530 Z= 0.239 Chirality : 0.039 0.153 1353 Planarity : 0.003 0.035 1464 Dihedral : 3.805 15.245 1149 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.34 % Allowed : 16.50 % Favored : 83.16 % 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: 0.38 (0.26), residues: 1082 helix: 2.13 (0.25), residues: 478 sheet: -1.51 (0.44), residues: 132 loop : -1.22 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 787 HIS 0.005 0.001 HIS A 672 PHE 0.021 0.001 PHE A 226 TYR 0.008 0.001 TYR A 219 ARG 0.002 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 1.008 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 44 average time/residue: 0.1574 time to fit residues: 11.6329 Evaluate side-chains 41 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0933 time to fit residues: 1.6113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.0070 chunk 71 optimal weight: 0.0370 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8494 Z= 0.171 Angle : 0.501 8.977 11530 Z= 0.243 Chirality : 0.039 0.151 1353 Planarity : 0.003 0.036 1464 Dihedral : 3.828 15.334 1149 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.46 % Allowed : 16.50 % Favored : 83.05 % 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: 0.45 (0.26), residues: 1082 helix: 2.17 (0.25), residues: 478 sheet: -1.45 (0.45), residues: 132 loop : -1.18 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1187 HIS 0.006 0.001 HIS A 672 PHE 0.021 0.001 PHE A 226 TYR 0.009 0.001 TYR A1057 ARG 0.002 0.000 ARG A 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.952 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 0.1608 time to fit residues: 10.9005 Evaluate side-chains 40 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1078 time to fit residues: 1.4358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 0.0040 chunk 10 optimal weight: 0.0010 chunk 15 optimal weight: 0.0000 chunk 76 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.081776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.062031 restraints weight = 23270.188| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.34 r_work: 0.2993 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 8494 Z= 0.112 Angle : 0.490 8.993 11530 Z= 0.235 Chirality : 0.038 0.149 1353 Planarity : 0.003 0.036 1464 Dihedral : 3.672 15.075 1149 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 17.06 % Favored : 82.94 % 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: 0.58 (0.26), residues: 1082 helix: 2.23 (0.25), residues: 477 sheet: -1.28 (0.45), residues: 132 loop : -1.09 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 787 HIS 0.004 0.000 HIS A 672 PHE 0.020 0.001 PHE A 226 TYR 0.007 0.001 TYR A 219 ARG 0.001 0.000 ARG A 383 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1643.32 seconds wall clock time: 30 minutes 40.28 seconds (1840.28 seconds total)