Starting phenix.real_space_refine on Thu Mar 14 17:22:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk8_14758/03_2024/7zk8_14758.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk8_14758/03_2024/7zk8_14758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk8_14758/03_2024/7zk8_14758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk8_14758/03_2024/7zk8_14758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk8_14758/03_2024/7zk8_14758.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk8_14758/03_2024/7zk8_14758.pdb" } resolution = 3.0 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= 0.013 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 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 5992 2.51 5 N 1569 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A GLU 1205": "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: 9331 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1192, 9331 Unusual residues: {' MG': 2, 'ATP': 2, 'JIZ': 1, 'Y01': 2} Inner-chain residues flagged as termini: ['pdbres="ALA A1271 "'] Classifications: {'peptide': 1181, 'undetermined': 7, 'water': 4} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 1151, None: 11} Not linked: pdbres="ALA A1271 " pdbres="ATP A2001 " Not linked: pdbres="ATP A2001 " pdbres=" MG A2002 " Not linked: pdbres=" MG A2002 " pdbres="ATP A2003 " Not linked: pdbres="ATP A2003 " pdbres=" MG A2004 " Not linked: pdbres=" MG A2004 " pdbres="JIZ A2005 " ... (remaining 6 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.75, per 1000 atoms: 0.62 Number of scatterers: 9331 At special positions: 0 Unit cell: (71.052, 86.523, 148.407, 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 36 16.00 P 6 15.00 Mg 2 11.99 O 1726 8.00 N 1569 7.00 C 5992 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.21 Conformation dependent library (CDL) restraints added in 1.7 seconds 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 70.4% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 43 through 62 Processing helix chain 'A' and resid 62 through 71 removed outlier: 3.594A pdb=" N PHE A 71 " --> pdb=" O MET A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 86 removed outlier: 3.685A pdb=" N SER A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.514A pdb=" N MET A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 92 through 154 removed outlier: 3.570A pdb=" N LYS A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 145 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.918A pdb=" N ASP A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 207 removed outlier: 4.060A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 256 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 265 through 320 removed outlier: 3.555A pdb=" N LYS A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 Processing helix chain 'A' and resid 336 through 367 Proline residue: A 346 - end of helix removed outlier: 3.899A pdb=" N TYR A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLU A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 528 through 543 removed outlier: 4.069A pdb=" N ARG A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 572 removed outlier: 3.797A pdb=" N ALA A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 removed outlier: 4.104A pdb=" N VAL A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 691 through 700 Processing helix chain 'A' and resid 703 through 737 removed outlier: 4.137A pdb=" N GLN A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'A' and resid 744 through 795 removed outlier: 4.061A pdb=" N LEU A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 795 " --> pdb=" O SER A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 801 removed outlier: 3.664A pdb=" N PHE A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 822 removed outlier: 4.064A pdb=" N ALA A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 826 through 850 removed outlier: 3.889A pdb=" N ALA A 830 " --> pdb=" O GLY A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 899 removed outlier: 4.132A pdb=" N VAL A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Proline residue: A 862 - end of helix removed outlier: 4.022A pdb=" N MET A 874 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 880 " --> pdb=" O SER A 876 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 906 Processing helix chain 'A' and resid 908 through 962 removed outlier: 4.708A pdb=" N ILE A 922 " --> pdb=" O GLN A 918 " (cutoff:3.500A) Proline residue: A 923 - end of helix Processing helix chain 'A' and resid 966 through 989 removed outlier: 3.618A pdb=" N VAL A 970 " --> pdb=" O THR A 966 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 989 " --> pdb=" O GLY A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1009 removed outlier: 3.561A pdb=" N VAL A 999 " --> pdb=" O ALA A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1080 removed outlier: 3.714A pdb=" N VAL A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1108 Processing helix chain 'A' and resid 1122 through 1129 Processing helix chain 'A' and resid 1137 through 1148 Processing helix chain 'A' and resid 1150 through 1157 Processing helix chain 'A' and resid 1159 through 1163 Processing helix chain 'A' and resid 1166 through 1170 Processing helix chain 'A' and resid 1173 through 1188 removed outlier: 4.154A pdb=" N ARG A1188 " --> pdb=" O ARG A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1217 removed outlier: 3.598A pdb=" N ALA A1217 " --> pdb=" O ALA A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1233 removed outlier: 3.730A pdb=" N THR A1232 " --> pdb=" O ARG A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1259 Processing helix chain 'A' and resid 1261 through 1268 Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 413 removed outlier: 6.538A pdb=" N LYS A 407 " --> pdb=" O HIS A 394 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N HIS A 394 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU A 409 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 393 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP A 444 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 469 removed outlier: 6.280A pdb=" N LEU A 548 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE A 581 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 550 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR A 418 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA A 595 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ALA A 420 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE A 597 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL A 422 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 594 " --> pdb=" O GLN A 605 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 605 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY A 596 " --> pdb=" O VAL A 603 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1053 through 1056 removed outlier: 5.487A pdb=" N PHE A1033 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE A1091 " --> pdb=" O PHE A1033 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY A1035 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER A1089 " --> pdb=" O GLY A1035 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1112 removed outlier: 6.199A pdb=" N LEU A1062 " --> pdb=" O VAL A1225 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N THR A1061 " --> pdb=" O LEU A1238 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL A1240 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA A1063 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE A1242 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A1065 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A1239 " --> pdb=" O HIS A1250 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS A1250 " --> pdb=" O ILE A1239 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A1241 " --> pdb=" O LYS A1248 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A1248 " --> pdb=" O VAL A1241 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1824 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: 3.25 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1521 1.31 - 1.44: 2454 1.44 - 1.56: 5450 1.56 - 1.69: 17 1.69 - 1.82: 64 Bond restraints: 9506 Sorted by residual: bond pdb=" C03 JIZ A2005 " pdb=" N02 JIZ A2005 " ideal model delta sigma weight residual 1.367 1.639 -0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" C08 JIZ A2005 " pdb=" N04 JIZ A2005 " ideal model delta sigma weight residual 1.366 1.617 -0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C13 JIZ A2005 " pdb=" N06 JIZ A2005 " ideal model delta sigma weight residual 1.366 1.617 -0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C02 JIZ A2005 " pdb=" S01 JIZ A2005 " ideal model delta sigma weight residual 1.728 1.546 0.182 2.00e-02 2.50e+03 8.29e+01 bond pdb=" C03 JIZ A2005 " pdb=" C04 JIZ A2005 " ideal model delta sigma weight residual 1.360 1.520 -0.160 2.00e-02 2.50e+03 6.40e+01 ... (remaining 9501 not shown) Histogram of bond angle deviations from ideal: 97.04 - 105.61: 168 105.61 - 114.18: 5605 114.18 - 122.74: 6359 122.74 - 131.31: 729 131.31 - 139.87: 19 Bond angle restraints: 12880 Sorted by residual: angle pdb=" N ASP A 76 " pdb=" CA ASP A 76 " pdb=" C ASP A 76 " ideal model delta sigma weight residual 111.36 101.04 10.32 1.09e+00 8.42e-01 8.96e+01 angle pdb=" N THR A 108 " pdb=" CA THR A 108 " pdb=" C THR A 108 " ideal model delta sigma weight residual 112.23 101.47 10.76 1.26e+00 6.30e-01 7.29e+01 angle pdb=" N ILE A 324 " pdb=" CA ILE A 324 " pdb=" C ILE A 324 " ideal model delta sigma weight residual 110.62 103.31 7.31 1.02e+00 9.61e-01 5.14e+01 angle pdb=" N ARG A 745 " pdb=" CA ARG A 745 " pdb=" C ARG A 745 " ideal model delta sigma weight residual 111.36 103.62 7.74 1.09e+00 8.42e-01 5.04e+01 angle pdb=" N PHE A 331 " pdb=" CA PHE A 331 " pdb=" C PHE A 331 " ideal model delta sigma weight residual 111.36 103.69 7.67 1.09e+00 8.42e-01 4.95e+01 ... (remaining 12875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.56: 5484 24.56 - 49.13: 266 49.13 - 73.69: 39 73.69 - 98.25: 11 98.25 - 122.81: 2 Dihedral angle restraints: 5802 sinusoidal: 2419 harmonic: 3383 Sorted by residual: dihedral pdb=" C GLN A 963 " pdb=" N GLN A 963 " pdb=" CA GLN A 963 " pdb=" CB GLN A 963 " ideal model delta harmonic sigma weight residual -122.60 -133.85 11.25 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" CBC Y01 A2007 " pdb=" CAR Y01 A2007 " pdb=" CAT Y01 A2007 " pdb=" CBH Y01 A2007 " ideal model delta sinusoidal sigma weight residual -57.13 65.68 -122.81 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" CA ALA A 582 " pdb=" C ALA A 582 " pdb=" N HIS A 583 " pdb=" CA HIS A 583 " ideal model delta harmonic sigma weight residual 180.00 160.60 19.40 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 5799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1292 0.073 - 0.147: 140 0.147 - 0.220: 24 0.220 - 0.294: 16 0.294 - 0.367: 6 Chirality restraints: 1478 Sorted by residual: chirality pdb=" CA GLN A 963 " pdb=" N GLN A 963 " pdb=" C GLN A 963 " pdb=" CB GLN A 963 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA MET A 99 " pdb=" N MET A 99 " pdb=" C MET A 99 " pdb=" CB MET A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA TRP A 208 " pdb=" N TRP A 208 " pdb=" C TRP A 208 " pdb=" CB TRP A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 1475 not shown) Planarity restraints: 1618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 65 " -0.018 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C PRO A 65 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO A 65 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU A 66 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 743 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C THR A 743 " -0.060 2.00e-02 2.50e+03 pdb=" O THR A 743 " 0.022 2.00e-02 2.50e+03 pdb=" N GLN A 744 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 207 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C GLY A 207 " -0.055 2.00e-02 2.50e+03 pdb=" O GLY A 207 " 0.020 2.00e-02 2.50e+03 pdb=" N TRP A 208 " 0.019 2.00e-02 2.50e+03 ... (remaining 1615 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 59 2.54 - 3.13: 7487 3.13 - 3.72: 14797 3.72 - 4.31: 21160 4.31 - 4.90: 34561 Nonbonded interactions: 78064 Sorted by model distance: nonbonded pdb="MG MG A2002 " pdb=" O HOH A2102 " model vdw 1.946 2.170 nonbonded pdb="MG MG A2002 " pdb=" O HOH A2101 " model vdw 1.975 2.170 nonbonded pdb=" O2G ATP A2003 " pdb="MG MG A2004 " model vdw 2.021 2.170 nonbonded pdb=" OE1 GLN A 471 " pdb="MG MG A2002 " model vdw 2.065 2.170 nonbonded pdb=" O2B ATP A2001 " pdb="MG MG A2002 " model vdw 2.092 2.170 ... (remaining 78059 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.470 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.700 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.009 0.272 9506 Z= 0.598 Angle : 0.969 17.564 12880 Z= 0.617 Chirality : 0.059 0.367 1478 Planarity : 0.005 0.066 1618 Dihedral : 14.592 122.813 3634 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.93 % Cbeta Deviations : 0.18 % 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: 0.60 (0.24), residues: 1177 helix: 0.95 (0.18), residues: 782 sheet: 0.35 (0.62), residues: 66 loop : -0.79 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 158 HIS 0.007 0.001 HIS A1003 PHE 0.017 0.002 PHE A 934 TYR 0.033 0.002 TYR A 114 ARG 0.007 0.001 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.057 Fit side-chains REVERT: A 315 SER cc_start: 0.8825 (t) cc_final: 0.8473 (m) REVERT: A 607 ASN cc_start: 0.7450 (t0) cc_final: 0.7206 (m110) REVERT: A 620 LYS cc_start: 0.8156 (mttt) cc_final: 0.7621 (ttpt) REVERT: A 955 PHE cc_start: 0.8642 (t80) cc_final: 0.8393 (t80) REVERT: A 960 VAL cc_start: 0.7758 (t) cc_final: 0.7489 (m) REVERT: A 1007 ILE cc_start: 0.8282 (tp) cc_final: 0.8018 (tp) REVERT: A 1244 ASN cc_start: 0.6847 (p0) cc_final: 0.6101 (t160) outliers start: 1 outliers final: 1 residues processed: 193 average time/residue: 1.0976 time to fit residues: 227.9093 Evaluate side-chains 122 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.0470 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 0.0570 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9506 Z= 0.162 Angle : 0.562 9.158 12880 Z= 0.293 Chirality : 0.042 0.231 1478 Planarity : 0.004 0.045 1618 Dihedral : 9.446 88.120 1512 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.00 % Allowed : 12.40 % Favored : 84.61 % 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: 1.28 (0.24), residues: 1177 helix: 1.55 (0.18), residues: 785 sheet: 0.72 (0.64), residues: 66 loop : -0.80 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 208 HIS 0.004 0.001 HIS A1003 PHE 0.017 0.001 PHE A 508 TYR 0.013 0.001 TYR A 312 ARG 0.003 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8255 (tm) cc_final: 0.8001 (tt) REVERT: A 315 SER cc_start: 0.8828 (t) cc_final: 0.8473 (m) REVERT: A 331 PHE cc_start: 0.7844 (m-80) cc_final: 0.7431 (m-80) REVERT: A 607 ASN cc_start: 0.7315 (t0) cc_final: 0.7079 (m110) REVERT: A 620 LYS cc_start: 0.8157 (mttt) cc_final: 0.7678 (ttpt) REVERT: A 955 PHE cc_start: 0.8619 (t80) cc_final: 0.8281 (t80) REVERT: A 960 VAL cc_start: 0.7801 (t) cc_final: 0.7574 (m) REVERT: A 1026 MET cc_start: 0.7296 (ppp) cc_final: 0.6560 (ttt) outliers start: 29 outliers final: 9 residues processed: 153 average time/residue: 0.9817 time to fit residues: 162.5512 Evaluate side-chains 125 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 116 optimal weight: 0.0570 chunk 96 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9506 Z= 0.158 Angle : 0.537 10.225 12880 Z= 0.276 Chirality : 0.041 0.239 1478 Planarity : 0.003 0.037 1618 Dihedral : 8.418 83.251 1510 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.48 % Allowed : 15.29 % Favored : 82.23 % 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: 1.45 (0.24), residues: 1177 helix: 1.66 (0.18), residues: 790 sheet: 0.68 (0.65), residues: 61 loop : -0.67 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 208 HIS 0.003 0.001 HIS A1003 PHE 0.012 0.001 PHE A 508 TYR 0.011 0.001 TYR A 110 ARG 0.004 0.000 ARG A 901 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.076 Fit side-chains REVERT: A 38 MET cc_start: 0.7963 (mtp) cc_final: 0.7652 (mtp) REVERT: A 64 LEU cc_start: 0.8274 (tm) cc_final: 0.7984 (tt) REVERT: A 315 SER cc_start: 0.8821 (t) cc_final: 0.8465 (m) REVERT: A 331 PHE cc_start: 0.7886 (m-80) cc_final: 0.7583 (m-80) REVERT: A 607 ASN cc_start: 0.7054 (t0) cc_final: 0.6825 (m110) REVERT: A 620 LYS cc_start: 0.8138 (mttt) cc_final: 0.7680 (ttpt) REVERT: A 955 PHE cc_start: 0.8586 (t80) cc_final: 0.8250 (t80) REVERT: A 960 VAL cc_start: 0.7760 (t) cc_final: 0.7523 (m) REVERT: A 1026 MET cc_start: 0.7295 (ppp) cc_final: 0.6582 (ttt) REVERT: A 1246 LYS cc_start: 0.7581 (mtpt) cc_final: 0.7139 (mmtt) outliers start: 24 outliers final: 10 residues processed: 133 average time/residue: 1.0321 time to fit residues: 148.8215 Evaluate side-chains 123 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 0.0870 chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 437 GLN ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9506 Z= 0.164 Angle : 0.520 8.575 12880 Z= 0.270 Chirality : 0.040 0.254 1478 Planarity : 0.003 0.040 1618 Dihedral : 8.101 83.598 1510 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.38 % Allowed : 17.05 % Favored : 80.58 % 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: 1.53 (0.24), residues: 1177 helix: 1.71 (0.18), residues: 792 sheet: 0.91 (0.65), residues: 61 loop : -0.64 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 208 HIS 0.003 0.001 HIS A1003 PHE 0.013 0.001 PHE A 508 TYR 0.011 0.001 TYR A 312 ARG 0.010 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 0.991 Fit side-chains REVERT: A 64 LEU cc_start: 0.8254 (tm) cc_final: 0.7987 (tt) REVERT: A 331 PHE cc_start: 0.7880 (m-80) cc_final: 0.7661 (m-80) REVERT: A 620 LYS cc_start: 0.8131 (mttt) cc_final: 0.7683 (ttpt) REVERT: A 955 PHE cc_start: 0.8590 (t80) cc_final: 0.8226 (t80) REVERT: A 960 VAL cc_start: 0.7750 (t) cc_final: 0.7500 (m) REVERT: A 1026 MET cc_start: 0.7269 (ppp) cc_final: 0.6604 (ttt) REVERT: A 1164 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7248 (ttp-110) REVERT: A 1246 LYS cc_start: 0.7536 (mtpt) cc_final: 0.7179 (mmtt) REVERT: A 1260 LYS cc_start: 0.7039 (mttm) cc_final: 0.6712 (mttp) outliers start: 23 outliers final: 10 residues processed: 129 average time/residue: 1.0729 time to fit residues: 149.6581 Evaluate side-chains 121 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1164 ARG Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9506 Z= 0.259 Angle : 0.555 8.224 12880 Z= 0.292 Chirality : 0.042 0.289 1478 Planarity : 0.003 0.040 1618 Dihedral : 8.277 83.809 1510 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.10 % Allowed : 17.87 % Favored : 79.03 % 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: 1.41 (0.24), residues: 1177 helix: 1.56 (0.18), residues: 794 sheet: 1.11 (0.67), residues: 62 loop : -0.60 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 208 HIS 0.005 0.001 HIS A 60 PHE 0.017 0.002 PHE A 508 TYR 0.017 0.001 TYR A 306 ARG 0.003 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 119 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8283 (tm) cc_final: 0.8018 (tt) REVERT: A 315 SER cc_start: 0.8869 (t) cc_final: 0.8501 (m) REVERT: A 331 PHE cc_start: 0.7921 (m-80) cc_final: 0.7654 (m-80) REVERT: A 506 TYR cc_start: 0.7713 (t80) cc_final: 0.7333 (t80) REVERT: A 510 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7662 (mpt) REVERT: A 620 LYS cc_start: 0.8161 (mttt) cc_final: 0.7685 (ttpt) REVERT: A 955 PHE cc_start: 0.8614 (t80) cc_final: 0.8294 (t80) REVERT: A 960 VAL cc_start: 0.7729 (t) cc_final: 0.7499 (m) REVERT: A 1026 MET cc_start: 0.7277 (ppp) cc_final: 0.6664 (ttt) REVERT: A 1164 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7280 (ttp-110) REVERT: A 1246 LYS cc_start: 0.7555 (mtpt) cc_final: 0.7204 (mmtt) outliers start: 30 outliers final: 16 residues processed: 137 average time/residue: 1.1151 time to fit residues: 166.2763 Evaluate side-chains 128 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1164 ARG Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 111 optimal weight: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN A 452 GLN A1050 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 9506 Z= 0.157 Angle : 0.517 9.004 12880 Z= 0.271 Chirality : 0.041 0.293 1478 Planarity : 0.003 0.042 1618 Dihedral : 8.074 86.614 1510 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.58 % Allowed : 19.63 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1177 helix: 1.74 (0.18), residues: 792 sheet: 1.05 (0.67), residues: 61 loop : -0.58 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 208 HIS 0.003 0.001 HIS A 60 PHE 0.015 0.001 PHE A 78 TYR 0.019 0.001 TYR A 949 ARG 0.004 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.099 Fit side-chains REVERT: A 64 LEU cc_start: 0.8251 (tm) cc_final: 0.8014 (tt) REVERT: A 331 PHE cc_start: 0.7905 (m-80) cc_final: 0.7609 (m-80) REVERT: A 584 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7546 (mtm-85) REVERT: A 620 LYS cc_start: 0.8116 (mttt) cc_final: 0.7664 (ttpt) REVERT: A 955 PHE cc_start: 0.8586 (t80) cc_final: 0.8258 (t80) REVERT: A 960 VAL cc_start: 0.7703 (t) cc_final: 0.7474 (m) REVERT: A 1026 MET cc_start: 0.7195 (ppp) cc_final: 0.6640 (ttt) REVERT: A 1164 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7304 (ttp-110) REVERT: A 1219 GLU cc_start: 0.7231 (mp0) cc_final: 0.7000 (mp0) REVERT: A 1246 LYS cc_start: 0.7531 (mtpt) cc_final: 0.7195 (mmtt) outliers start: 25 outliers final: 11 residues processed: 128 average time/residue: 1.1136 time to fit residues: 153.8640 Evaluate side-chains 117 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ARG Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1164 ARG Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN A 452 GLN ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9506 Z= 0.166 Angle : 0.516 7.203 12880 Z= 0.271 Chirality : 0.041 0.331 1478 Planarity : 0.003 0.042 1618 Dihedral : 7.928 80.514 1510 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.17 % Allowed : 20.76 % Favored : 77.07 % 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: 1.61 (0.24), residues: 1177 helix: 1.73 (0.18), residues: 795 sheet: 0.86 (0.66), residues: 63 loop : -0.53 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 208 HIS 0.003 0.001 HIS A 60 PHE 0.016 0.001 PHE A 724 TYR 0.015 0.001 TYR A 306 ARG 0.007 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 1.018 Fit side-chains REVERT: A 64 LEU cc_start: 0.8266 (tm) cc_final: 0.8015 (tt) REVERT: A 331 PHE cc_start: 0.7884 (m-80) cc_final: 0.7538 (m-80) REVERT: A 584 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7522 (mtm-85) REVERT: A 605 GLN cc_start: 0.7372 (tt0) cc_final: 0.7172 (mt0) REVERT: A 620 LYS cc_start: 0.8147 (mttt) cc_final: 0.7692 (ttpt) REVERT: A 955 PHE cc_start: 0.8580 (t80) cc_final: 0.8243 (t80) REVERT: A 960 VAL cc_start: 0.7721 (t) cc_final: 0.7497 (m) REVERT: A 1026 MET cc_start: 0.7209 (ppp) cc_final: 0.6664 (ttt) REVERT: A 1246 LYS cc_start: 0.7504 (mtpt) cc_final: 0.7189 (mmtt) outliers start: 21 outliers final: 13 residues processed: 128 average time/residue: 1.0978 time to fit residues: 151.9075 Evaluate side-chains 122 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ARG Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 100 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN A 452 GLN ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 9506 Z= 0.155 Angle : 0.513 7.781 12880 Z= 0.270 Chirality : 0.041 0.341 1478 Planarity : 0.003 0.043 1618 Dihedral : 7.841 84.818 1510 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.65 % Allowed : 21.80 % Favored : 76.55 % 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: 1.66 (0.24), residues: 1177 helix: 1.79 (0.18), residues: 795 sheet: 0.83 (0.65), residues: 63 loop : -0.56 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 208 HIS 0.003 0.001 HIS A 60 PHE 0.018 0.001 PHE A 724 TYR 0.014 0.001 TYR A 306 ARG 0.007 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8228 (tm) cc_final: 0.7978 (tt) REVERT: A 331 PHE cc_start: 0.7845 (m-80) cc_final: 0.7526 (m-80) REVERT: A 620 LYS cc_start: 0.8133 (mttt) cc_final: 0.7676 (ttpt) REVERT: A 944 MET cc_start: 0.7117 (tmm) cc_final: 0.6707 (tmm) REVERT: A 955 PHE cc_start: 0.8566 (t80) cc_final: 0.8234 (t80) REVERT: A 1026 MET cc_start: 0.7197 (ppp) cc_final: 0.6677 (ttt) REVERT: A 1086 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6050 (ptp) REVERT: A 1246 LYS cc_start: 0.7460 (mtpt) cc_final: 0.7180 (mmtt) outliers start: 16 outliers final: 11 residues processed: 127 average time/residue: 1.0135 time to fit residues: 139.5589 Evaluate side-chains 122 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ARG Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1086 MET Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 0.0370 chunk 32 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN A 605 GLN ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9506 Z= 0.158 Angle : 0.516 8.825 12880 Z= 0.271 Chirality : 0.041 0.365 1478 Planarity : 0.003 0.043 1618 Dihedral : 7.765 87.348 1510 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.65 % Allowed : 22.62 % Favored : 75.72 % 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: 1.72 (0.24), residues: 1177 helix: 1.84 (0.18), residues: 795 sheet: 0.85 (0.65), residues: 63 loop : -0.56 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 208 HIS 0.003 0.001 HIS A 60 PHE 0.025 0.001 PHE A 763 TYR 0.015 0.001 TYR A 306 ARG 0.007 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8231 (tm) cc_final: 0.7976 (tt) REVERT: A 74 MET cc_start: 0.3297 (tpt) cc_final: 0.1181 (tmt) REVERT: A 331 PHE cc_start: 0.7804 (m-80) cc_final: 0.7468 (m-80) REVERT: A 620 LYS cc_start: 0.8123 (mttt) cc_final: 0.7662 (ttpt) REVERT: A 755 PHE cc_start: 0.7273 (m-80) cc_final: 0.6892 (t80) REVERT: A 944 MET cc_start: 0.7090 (tmm) cc_final: 0.6696 (tmm) REVERT: A 955 PHE cc_start: 0.8561 (t80) cc_final: 0.8232 (t80) REVERT: A 1026 MET cc_start: 0.7207 (ppp) cc_final: 0.6695 (ttt) REVERT: A 1246 LYS cc_start: 0.7463 (mtpt) cc_final: 0.7187 (mmtt) outliers start: 16 outliers final: 11 residues processed: 115 average time/residue: 1.0603 time to fit residues: 132.2242 Evaluate side-chains 117 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ARG Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 100 optimal weight: 0.0050 chunk 28 optimal weight: 10.0000 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9506 Z= 0.181 Angle : 0.526 8.511 12880 Z= 0.277 Chirality : 0.041 0.344 1478 Planarity : 0.003 0.043 1618 Dihedral : 7.813 86.355 1510 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.34 % Allowed : 22.73 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.24), residues: 1177 helix: 1.78 (0.18), residues: 796 sheet: 0.83 (0.66), residues: 63 loop : -0.58 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 208 HIS 0.003 0.001 HIS A 60 PHE 0.022 0.001 PHE A 763 TYR 0.014 0.001 TYR A 306 ARG 0.007 0.000 ARG A 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8232 (tm) cc_final: 0.7965 (tt) REVERT: A 74 MET cc_start: 0.3221 (tpt) cc_final: 0.1201 (tmt) REVERT: A 331 PHE cc_start: 0.7791 (m-80) cc_final: 0.7467 (m-80) REVERT: A 620 LYS cc_start: 0.8138 (mttt) cc_final: 0.7630 (ttpp) REVERT: A 755 PHE cc_start: 0.7275 (m-80) cc_final: 0.6946 (t80) REVERT: A 944 MET cc_start: 0.7082 (tmm) cc_final: 0.6648 (tmm) REVERT: A 955 PHE cc_start: 0.8572 (t80) cc_final: 0.8287 (t80) REVERT: A 1026 MET cc_start: 0.7185 (ppp) cc_final: 0.6717 (ttt) REVERT: A 1246 LYS cc_start: 0.7469 (mtpt) cc_final: 0.7217 (mmtt) outliers start: 13 outliers final: 13 residues processed: 114 average time/residue: 1.1133 time to fit residues: 137.2944 Evaluate side-chains 117 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ARG Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1238 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.163253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120451 restraints weight = 10963.899| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.17 r_work: 0.3301 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9506 Z= 0.183 Angle : 0.528 9.130 12880 Z= 0.277 Chirality : 0.042 0.364 1478 Planarity : 0.003 0.043 1618 Dihedral : 7.813 86.105 1510 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.34 % Allowed : 22.83 % Favored : 75.83 % 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: 1.65 (0.24), residues: 1177 helix: 1.79 (0.18), residues: 796 sheet: 0.80 (0.66), residues: 63 loop : -0.58 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 208 HIS 0.003 0.001 HIS A 60 PHE 0.023 0.001 PHE A 763 TYR 0.015 0.001 TYR A 306 ARG 0.006 0.000 ARG A 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3532.93 seconds wall clock time: 63 minutes 4.27 seconds (3784.27 seconds total)