Starting phenix.real_space_refine on Tue Sep 24 06:16:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vul_43532/09_2024/8vul_43532.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vul_43532/09_2024/8vul_43532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vul_43532/09_2024/8vul_43532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vul_43532/09_2024/8vul_43532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vul_43532/09_2024/8vul_43532.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vul_43532/09_2024/8vul_43532.cif" } resolution = 3.83 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= 0.024 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 4560 2.51 5 N 1244 2.21 5 O 1329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7158 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2800 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 17, 'TRANS': 351} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'ASP:plan': 1, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2665 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 15, 'TRANS': 350} Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 15, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 168 Chain: "H" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 894 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 799 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 102} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 5.41, per 1000 atoms: 0.76 Number of scatterers: 7158 At special positions: 0 Unit cell: (107.8, 126.5, 85.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1329 8.00 N 1244 7.00 C 4560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.04 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1790 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 12 sheets defined 29.2% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.792A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 86 removed outlier: 4.442A pdb=" N ALA A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.624A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.862A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 170 through 186 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.779A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.853A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.935A pdb=" N LEU A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 260 " --> pdb=" O ASN A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 277 through 296 Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 78 through 94 removed outlier: 3.682A pdb=" N ILE B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 4.304A pdb=" N GLN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.757A pdb=" N MET B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 165 removed outlier: 3.507A pdb=" N GLN B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 232 through 247 Processing helix chain 'B' and resid 287 through 310 Processing helix chain 'H' and resid 62 through 68 removed outlier: 3.638A pdb=" N LYS H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N SER H 66 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL H 68 " --> pdb=" O LYS H 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.881A pdb=" N ASP L 85 " --> pdb=" O LYS L 82 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU L 86 " --> pdb=" O THR L 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 82 through 86' Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.423A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 4.092A pdb=" N LYS A 193 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.178A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 70 removed outlier: 9.340A pdb=" N VAL B 99 " --> pdb=" O ASN B 35 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA B 37 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLY B 101 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N MET B 39 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.248A pdb=" N ILE B 227 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL B 279 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B 363 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS B 377 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER B 384 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.439A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP H 35 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N CYS H 96 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TRP H 110 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ARG H 98 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.439A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP H 35 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.544A pdb=" N THR L 5 " --> pdb=" O THR L 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.805A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.557A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER L 93 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL L 100 " --> pdb=" O SER L 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 63 through 64 258 hydrogen bonds defined for protein. 720 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: 1.89 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2329 1.35 - 1.47: 1858 1.47 - 1.59: 3097 1.59 - 1.72: 2 1.72 - 1.84: 41 Bond restraints: 7327 Sorted by residual: bond pdb=" N PRO A 304 " pdb=" CA PRO A 304 " ideal model delta sigma weight residual 1.465 1.407 0.058 2.03e-02 2.43e+03 8.25e+00 bond pdb=" CB PRO A 304 " pdb=" CG PRO A 304 " ideal model delta sigma weight residual 1.492 1.635 -0.143 5.00e-02 4.00e+02 8.23e+00 bond pdb=" CG PRO A 304 " pdb=" CD PRO A 304 " ideal model delta sigma weight residual 1.503 1.408 0.095 3.40e-02 8.65e+02 7.74e+00 bond pdb=" N PRO A 304 " pdb=" CD PRO A 304 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 5.78e+00 bond pdb=" CB PRO B 336 " pdb=" CG PRO B 336 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.78e+00 ... (remaining 7322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 9950 3.19 - 6.37: 42 6.37 - 9.56: 14 9.56 - 12.75: 2 12.75 - 15.94: 1 Bond angle restraints: 10009 Sorted by residual: angle pdb=" CA PRO A 304 " pdb=" N PRO A 304 " pdb=" CD PRO A 304 " ideal model delta sigma weight residual 112.00 96.06 15.94 1.40e+00 5.10e-01 1.30e+02 angle pdb=" CA PRO B 336 " pdb=" N PRO B 336 " pdb=" CD PRO B 336 " ideal model delta sigma weight residual 112.00 102.92 9.08 1.40e+00 5.10e-01 4.21e+01 angle pdb=" N PRO A 304 " pdb=" CD PRO A 304 " pdb=" CG PRO A 304 " ideal model delta sigma weight residual 103.20 94.35 8.85 1.50e+00 4.44e-01 3.48e+01 angle pdb=" C SER B 225 " pdb=" N VAL B 226 " pdb=" CA VAL B 226 " ideal model delta sigma weight residual 121.95 129.15 -7.20 1.53e+00 4.27e-01 2.21e+01 angle pdb=" N PRO B 336 " pdb=" CD PRO B 336 " pdb=" CG PRO B 336 " ideal model delta sigma weight residual 103.20 96.36 6.84 1.50e+00 4.44e-01 2.08e+01 ... (remaining 10004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3690 17.92 - 35.84: 478 35.84 - 53.76: 119 53.76 - 71.68: 18 71.68 - 89.60: 7 Dihedral angle restraints: 4312 sinusoidal: 1531 harmonic: 2781 Sorted by residual: dihedral pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " pdb=" SG CYS A 308 " pdb=" CB CYS A 308 " ideal model delta sinusoidal sigma weight residual -86.00 -28.09 -57.91 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CA SER B 225 " pdb=" C SER B 225 " pdb=" N VAL B 226 " pdb=" CA VAL B 226 " ideal model delta harmonic sigma weight residual 180.00 153.09 26.91 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA PRO A 98 " pdb=" C PRO A 98 " pdb=" N ASN A 99 " pdb=" CA ASN A 99 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 4309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 739 0.032 - 0.065: 274 0.065 - 0.097: 100 0.097 - 0.129: 43 0.129 - 0.161: 7 Chirality restraints: 1163 Sorted by residual: chirality pdb=" CA VAL B 226 " pdb=" N VAL B 226 " pdb=" C VAL B 226 " pdb=" CB VAL B 226 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA ASN L 53 " pdb=" N ASN L 53 " pdb=" C ASN L 53 " pdb=" CB ASN L 53 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA VAL A 32 " pdb=" N VAL A 32 " pdb=" C VAL A 32 " pdb=" CB VAL A 32 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 1160 not shown) Planarity restraints: 1274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 303 " -0.117 5.00e-02 4.00e+02 1.64e-01 4.29e+01 pdb=" N PRO A 304 " 0.283 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 204 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C VAL A 204 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL A 204 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 205 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 63 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 64 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 64 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 64 " -0.025 5.00e-02 4.00e+02 ... (remaining 1271 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 958 2.75 - 3.29: 6671 3.29 - 3.83: 10992 3.83 - 4.36: 11212 4.36 - 4.90: 21177 Nonbonded interactions: 51010 Sorted by model distance: nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 77 " model vdw 2.218 3.040 nonbonded pdb=" O ILE B 116 " pdb=" OG1 THR B 120 " model vdw 2.233 3.040 nonbonded pdb=" O SER H 32 " pdb=" OG SER H 32 " model vdw 2.236 3.040 nonbonded pdb=" NE1 TRP H 106 " pdb=" OG1 THR L 47 " model vdw 2.270 3.120 nonbonded pdb=" OD1 ASN B 367 " pdb=" N LYS B 368 " model vdw 2.290 3.120 ... (remaining 51005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.950 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 0.143 7327 Z= 0.243 Angle : 0.680 15.935 10009 Z= 0.363 Chirality : 0.042 0.161 1163 Planarity : 0.006 0.164 1274 Dihedral : 16.798 89.605 2510 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.80 % Favored : 90.89 % Rotamer: Outliers : 0.27 % Allowed : 35.74 % Favored : 63.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.27), residues: 955 helix: 1.71 (0.36), residues: 234 sheet: -1.14 (0.36), residues: 209 loop : -2.59 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 255 HIS 0.003 0.001 HIS A 53 PHE 0.013 0.001 PHE B 396 TYR 0.012 0.001 TYR L 94 ARG 0.004 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 0.794 Fit side-chains REVERT: A 172 GLU cc_start: 0.7274 (mp0) cc_final: 0.6961 (mp0) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.1476 time to fit residues: 29.7023 Evaluate side-chains 134 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 72 optimal weight: 0.0040 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.0270 chunk 84 optimal weight: 2.9990 overall best weight: 1.0056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 177 GLN A 196 GLN A 358 ASN H 105 ASN L 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7327 Z= 0.297 Angle : 0.658 10.908 10009 Z= 0.342 Chirality : 0.044 0.147 1163 Planarity : 0.005 0.046 1274 Dihedral : 4.444 27.786 1027 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.16 % Favored : 89.53 % Rotamer: Outliers : 5.05 % Allowed : 32.47 % Favored : 62.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.27), residues: 955 helix: 1.89 (0.35), residues: 239 sheet: -1.33 (0.34), residues: 228 loop : -2.61 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 34 HIS 0.004 0.001 HIS H 54 PHE 0.020 0.002 PHE B 186 TYR 0.012 0.001 TYR H 53 ARG 0.005 0.001 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 0.820 Fit side-chains REVERT: A 323 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7212 (mtm-85) REVERT: B 193 ASN cc_start: 0.7349 (t0) cc_final: 0.6895 (t0) REVERT: B 286 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.7058 (t80) outliers start: 37 outliers final: 25 residues processed: 164 average time/residue: 0.1513 time to fit residues: 35.3822 Evaluate side-chains 147 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.0010 chunk 26 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 83 optimal weight: 0.0870 chunk 28 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 overall best weight: 0.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 ASN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7327 Z= 0.165 Angle : 0.599 9.923 10009 Z= 0.310 Chirality : 0.042 0.156 1163 Planarity : 0.004 0.045 1274 Dihedral : 4.284 32.108 1027 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.38 % Favored : 91.31 % Rotamer: Outliers : 4.37 % Allowed : 31.38 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.28), residues: 955 helix: 1.82 (0.35), residues: 245 sheet: -1.28 (0.33), residues: 238 loop : -2.63 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 106 HIS 0.003 0.001 HIS A 53 PHE 0.016 0.001 PHE B 396 TYR 0.011 0.001 TYR L 89 ARG 0.004 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: B 286 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.6996 (t80) REVERT: B 365 VAL cc_start: 0.9260 (p) cc_final: 0.8960 (m) outliers start: 32 outliers final: 15 residues processed: 158 average time/residue: 0.1457 time to fit residues: 33.1109 Evaluate side-chains 141 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7327 Z= 0.249 Angle : 0.628 10.109 10009 Z= 0.325 Chirality : 0.043 0.154 1163 Planarity : 0.004 0.045 1274 Dihedral : 4.304 29.334 1027 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.42 % Favored : 90.26 % Rotamer: Outliers : 5.05 % Allowed : 29.88 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.28), residues: 955 helix: 1.78 (0.35), residues: 245 sheet: -1.23 (0.34), residues: 234 loop : -2.69 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 247 HIS 0.003 0.001 HIS B 42 PHE 0.013 0.001 PHE B 186 TYR 0.009 0.001 TYR A 367 ARG 0.003 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 0.807 Fit side-chains REVERT: A 323 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7252 (mtm-85) REVERT: A 326 MET cc_start: 0.7634 (mmm) cc_final: 0.7263 (mmm) REVERT: B 193 ASN cc_start: 0.7451 (t0) cc_final: 0.6852 (t0) REVERT: B 244 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7630 (ttt90) REVERT: B 286 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7193 (t80) REVERT: H 64 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8003 (pp) outliers start: 37 outliers final: 25 residues processed: 159 average time/residue: 0.1453 time to fit residues: 33.0210 Evaluate side-chains 149 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7327 Z= 0.244 Angle : 0.625 10.037 10009 Z= 0.324 Chirality : 0.043 0.151 1163 Planarity : 0.004 0.044 1274 Dihedral : 4.389 29.503 1027 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.84 % Favored : 89.84 % Rotamer: Outliers : 5.87 % Allowed : 30.29 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.28), residues: 955 helix: 1.84 (0.35), residues: 246 sheet: -1.23 (0.34), residues: 234 loop : -2.69 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 381 HIS 0.003 0.001 HIS A 53 PHE 0.012 0.001 PHE B 186 TYR 0.010 0.001 TYR A 367 ARG 0.003 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 81 ASP cc_start: 0.5263 (OUTLIER) cc_final: 0.4383 (p0) REVERT: A 323 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7290 (mtm-85) REVERT: A 326 MET cc_start: 0.7488 (mmm) cc_final: 0.7163 (mmm) REVERT: B 193 ASN cc_start: 0.7562 (t0) cc_final: 0.7028 (t0) REVERT: B 286 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7332 (t80) REVERT: H 64 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7935 (pp) outliers start: 43 outliers final: 27 residues processed: 159 average time/residue: 0.1447 time to fit residues: 32.8696 Evaluate side-chains 151 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 52 optimal weight: 0.0020 chunk 22 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7327 Z= 0.192 Angle : 0.615 9.849 10009 Z= 0.318 Chirality : 0.043 0.145 1163 Planarity : 0.004 0.045 1274 Dihedral : 4.280 31.511 1027 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.21 % Favored : 90.47 % Rotamer: Outliers : 5.32 % Allowed : 31.11 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.28), residues: 955 helix: 1.87 (0.35), residues: 245 sheet: -1.18 (0.34), residues: 234 loop : -2.63 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 255 HIS 0.003 0.001 HIS A 53 PHE 0.012 0.001 PHE B 186 TYR 0.010 0.001 TYR L 94 ARG 0.003 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 0.823 Fit side-chains REVERT: A 323 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7214 (mtm-85) REVERT: A 326 MET cc_start: 0.7366 (mmm) cc_final: 0.7117 (mmm) REVERT: B 193 ASN cc_start: 0.7515 (t0) cc_final: 0.7001 (t0) REVERT: B 286 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7257 (t80) REVERT: B 365 VAL cc_start: 0.9296 (p) cc_final: 0.9014 (m) REVERT: H 64 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.7983 (pp) outliers start: 39 outliers final: 25 residues processed: 149 average time/residue: 0.1485 time to fit residues: 31.8636 Evaluate side-chains 150 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 91 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 65 optimal weight: 0.0060 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 54 optimal weight: 0.0670 chunk 41 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7327 Z= 0.179 Angle : 0.606 9.727 10009 Z= 0.313 Chirality : 0.042 0.143 1163 Planarity : 0.004 0.044 1274 Dihedral : 4.177 30.707 1027 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.01 % Favored : 90.68 % Rotamer: Outliers : 4.09 % Allowed : 32.06 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.49 (0.28), residues: 955 helix: 1.90 (0.35), residues: 245 sheet: -1.14 (0.34), residues: 239 loop : -2.61 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 35 HIS 0.004 0.001 HIS A 53 PHE 0.015 0.001 PHE B 186 TYR 0.016 0.001 TYR L 89 ARG 0.003 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 0.799 Fit side-chains REVERT: A 323 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7255 (mtm-85) REVERT: A 385 GLU cc_start: 0.7834 (pm20) cc_final: 0.7592 (pm20) REVERT: B 193 ASN cc_start: 0.7517 (t0) cc_final: 0.7003 (t0) REVERT: B 286 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7367 (t80) REVERT: H 64 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.7980 (pp) outliers start: 30 outliers final: 25 residues processed: 149 average time/residue: 0.1410 time to fit residues: 31.0010 Evaluate side-chains 146 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 91 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 0.0050 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 70 optimal weight: 0.0470 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.3892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7327 Z= 0.181 Angle : 0.608 9.672 10009 Z= 0.313 Chirality : 0.042 0.140 1163 Planarity : 0.004 0.045 1274 Dihedral : 4.152 31.290 1027 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.32 % Favored : 90.37 % Rotamer: Outliers : 5.32 % Allowed : 32.20 % Favored : 62.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.48 (0.28), residues: 955 helix: 1.92 (0.35), residues: 245 sheet: -1.16 (0.34), residues: 239 loop : -2.59 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 35 HIS 0.003 0.001 HIS A 53 PHE 0.014 0.001 PHE B 186 TYR 0.010 0.001 TYR L 94 ARG 0.003 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 172 GLU cc_start: 0.7430 (mp0) cc_final: 0.7085 (mp0) REVERT: A 323 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7232 (mtm-85) REVERT: A 379 ILE cc_start: 0.8985 (pt) cc_final: 0.8686 (pt) REVERT: B 193 ASN cc_start: 0.7543 (t0) cc_final: 0.7048 (t0) REVERT: B 286 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7367 (t80) REVERT: B 315 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: H 20 LEU cc_start: 0.8546 (mt) cc_final: 0.8255 (mp) REVERT: H 64 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.7960 (pp) outliers start: 39 outliers final: 25 residues processed: 158 average time/residue: 0.1453 time to fit residues: 33.2767 Evaluate side-chains 152 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 123 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 91 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 88 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7327 Z= 0.215 Angle : 0.642 9.793 10009 Z= 0.329 Chirality : 0.042 0.170 1163 Planarity : 0.004 0.044 1274 Dihedral : 4.149 27.615 1027 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.53 % Favored : 90.16 % Rotamer: Outliers : 4.77 % Allowed : 32.33 % Favored : 62.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.28), residues: 955 helix: 1.91 (0.35), residues: 245 sheet: -1.15 (0.34), residues: 234 loop : -2.63 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 255 HIS 0.003 0.001 HIS A 53 PHE 0.014 0.001 PHE B 186 TYR 0.010 0.001 TYR L 50 ARG 0.003 0.000 ARG L 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 0.738 Fit side-chains REVERT: A 227 ASP cc_start: 0.8161 (p0) cc_final: 0.7149 (p0) REVERT: A 323 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7257 (mtm-85) REVERT: A 385 GLU cc_start: 0.7873 (pm20) cc_final: 0.7625 (pm20) REVERT: B 193 ASN cc_start: 0.7566 (t0) cc_final: 0.7098 (t0) REVERT: B 286 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7414 (t80) REVERT: B 315 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: H 20 LEU cc_start: 0.8521 (mt) cc_final: 0.8257 (mp) REVERT: H 64 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7968 (pp) REVERT: L 90 TYR cc_start: 0.8420 (m-80) cc_final: 0.8080 (m-80) outliers start: 35 outliers final: 27 residues processed: 153 average time/residue: 0.1481 time to fit residues: 32.5326 Evaluate side-chains 147 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7327 Z= 0.272 Angle : 0.677 10.111 10009 Z= 0.349 Chirality : 0.043 0.189 1163 Planarity : 0.004 0.044 1274 Dihedral : 4.347 25.514 1027 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.05 % Favored : 89.63 % Rotamer: Outliers : 4.77 % Allowed : 32.20 % Favored : 63.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.56 (0.28), residues: 955 helix: 1.86 (0.35), residues: 245 sheet: -1.19 (0.34), residues: 234 loop : -2.65 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 110 HIS 0.003 0.001 HIS B 42 PHE 0.017 0.001 PHE B 186 TYR 0.010 0.001 TYR B 286 ARG 0.003 0.000 ARG L 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 0.760 Fit side-chains REVERT: A 80 GLU cc_start: 0.5376 (tm-30) cc_final: 0.5051 (tm-30) REVERT: A 323 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7334 (mtm-85) REVERT: B 193 ASN cc_start: 0.7580 (t0) cc_final: 0.7208 (t0) REVERT: B 286 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7520 (t80) REVERT: B 315 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: H 20 LEU cc_start: 0.8599 (mt) cc_final: 0.8342 (mp) REVERT: H 64 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8000 (pp) outliers start: 35 outliers final: 29 residues processed: 146 average time/residue: 0.1428 time to fit residues: 30.0529 Evaluate side-chains 144 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 0.0270 chunk 75 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 0.0870 chunk 4 optimal weight: 0.9980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112037 restraints weight = 11516.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112789 restraints weight = 9563.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114502 restraints weight = 8736.644| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 0.037 7327 Z= 0.185 Angle : 0.645 9.870 10009 Z= 0.329 Chirality : 0.043 0.174 1163 Planarity : 0.004 0.044 1274 Dihedral : 4.189 27.077 1027 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.32 % Favored : 90.37 % Rotamer: Outliers : 4.50 % Allowed : 32.61 % Favored : 62.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.52 (0.28), residues: 955 helix: 1.89 (0.35), residues: 245 sheet: -1.15 (0.34), residues: 234 loop : -2.62 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.004 0.001 HIS A 53 PHE 0.015 0.001 PHE B 396 TYR 0.010 0.001 TYR L 50 ARG 0.002 0.000 ARG L 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1729.91 seconds wall clock time: 31 minutes 37.93 seconds (1897.93 seconds total)