Starting phenix.real_space_refine on Fri Nov 15 12:24:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u58_41914/11_2024/8u58_41914.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u58_41914/11_2024/8u58_41914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u58_41914/11_2024/8u58_41914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u58_41914/11_2024/8u58_41914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u58_41914/11_2024/8u58_41914.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u58_41914/11_2024/8u58_41914.cif" } resolution = 2.45 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= 0.027 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 56 5.16 5 C 5962 2.51 5 N 1362 2.21 5 O 1504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8884 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4428 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C Time building chain proxies: 8.23, per 1000 atoms: 0.93 Number of scatterers: 8884 At special positions: 0 Unit cell: (130.491, 99.5598, 69.5952, 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 56 16.00 O 1504 8.00 N 1362 7.00 C 5962 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 - 3.00 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 309 " " NAG C 901 " - " ASN C 309 " Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 89.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 41 through 62 Processing helix chain 'C' and resid 66 through 80 removed outlier: 3.612A pdb=" N LYS C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 73 " --> pdb=" O GLN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 93 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.508A pdb=" N VAL C 98 " --> pdb=" O PHE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 125 Processing helix chain 'C' and resid 129 through 141 Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 149 through 159 removed outlier: 3.507A pdb=" N ILE C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 165 Processing helix chain 'C' and resid 166 through 196 removed outlier: 4.134A pdb=" N TYR C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Proline residue: C 174 - end of helix Proline residue: C 182 - end of helix Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 217 through 233 removed outlier: 3.587A pdb=" N VAL C 223 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 264 removed outlier: 4.223A pdb=" N ASN C 243 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE C 244 " --> pdb=" O TYR C 240 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY C 254 " --> pdb=" O ASN C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 288 Processing helix chain 'C' and resid 288 through 302 Processing helix chain 'C' and resid 306 through 322 Processing helix chain 'C' and resid 326 through 337 removed outlier: 4.170A pdb=" N ALA C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 367 removed outlier: 3.673A pdb=" N ALA C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) Proline residue: C 356 - end of helix Processing helix chain 'C' and resid 368 through 370 No H-bonds generated for 'chain 'C' and resid 368 through 370' Processing helix chain 'C' and resid 371 through 404 Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 411 through 436 removed outlier: 4.101A pdb=" N PHE C 434 " --> pdb=" O MET C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 472 removed outlier: 3.914A pdb=" N LEU C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 503 removed outlier: 4.197A pdb=" N ILE C 491 " --> pdb=" O SER C 487 " (cutoff:3.500A) Proline residue: C 492 - end of helix Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 516 through 542 Processing helix chain 'C' and resid 654 through 682 Processing helix chain 'C' and resid 688 through 712 removed outlier: 5.656A pdb=" N GLY C 704 " --> pdb=" O ASN C 700 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N PHE C 705 " --> pdb=" O PHE C 701 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 706 " --> pdb=" O GLY C 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.603A pdb=" N LYS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.522A pdb=" N VAL A 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 125 Processing helix chain 'A' and resid 129 through 141 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.505A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 166 through 196 removed outlier: 4.134A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.582A pdb=" N VAL A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 264 removed outlier: 4.219A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 326 through 337 removed outlier: 4.176A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.681A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 411 through 436 removed outlier: 4.099A pdb=" N PHE A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 472 removed outlier: 3.911A pdb=" N LEU A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 503 removed outlier: 4.196A pdb=" N ILE A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 516 through 542 Processing helix chain 'A' and resid 654 through 682 Processing helix chain 'A' and resid 688 through 712 removed outlier: 5.652A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2350 1.34 - 1.45: 1673 1.45 - 1.57: 4981 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 9094 Sorted by residual: bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.45e+00 bond pdb=" C1 NAG C 901 " pdb=" O5 NAG C 901 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" CB TYR C 320 " pdb=" CG TYR C 320 " ideal model delta sigma weight residual 1.512 1.465 0.047 2.20e-02 2.07e+03 4.59e+00 bond pdb=" CB TYR A 320 " pdb=" CG TYR A 320 " ideal model delta sigma weight residual 1.512 1.465 0.047 2.20e-02 2.07e+03 4.49e+00 bond pdb=" C PRO A 372 " pdb=" N LYS A 373 " ideal model delta sigma weight residual 1.337 1.305 0.032 1.61e-02 3.86e+03 4.03e+00 ... (remaining 9089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 11528 1.89 - 3.78: 708 3.78 - 5.68: 92 5.68 - 7.57: 18 7.57 - 9.46: 10 Bond angle restraints: 12356 Sorted by residual: angle pdb=" CA TYR C 451 " pdb=" CB TYR C 451 " pdb=" CG TYR C 451 " ideal model delta sigma weight residual 113.90 104.44 9.46 1.80e+00 3.09e-01 2.76e+01 angle pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " pdb=" CG TYR A 451 " ideal model delta sigma weight residual 113.90 104.47 9.43 1.80e+00 3.09e-01 2.75e+01 angle pdb=" CA TYR A 689 " pdb=" CB TYR A 689 " pdb=" CG TYR A 689 " ideal model delta sigma weight residual 113.90 106.06 7.84 1.80e+00 3.09e-01 1.90e+01 angle pdb=" CA TYR C 689 " pdb=" CB TYR C 689 " pdb=" CG TYR C 689 " ideal model delta sigma weight residual 113.90 106.08 7.82 1.80e+00 3.09e-01 1.89e+01 angle pdb=" CA TYR C 320 " pdb=" CB TYR C 320 " pdb=" CG TYR C 320 " ideal model delta sigma weight residual 113.90 106.76 7.14 1.80e+00 3.09e-01 1.57e+01 ... (remaining 12351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 4953 16.92 - 33.83: 323 33.83 - 50.75: 36 50.75 - 67.66: 10 67.66 - 84.58: 4 Dihedral angle restraints: 5326 sinusoidal: 2050 harmonic: 3276 Sorted by residual: dihedral pdb=" CA ASN A 63 " pdb=" C ASN A 63 " pdb=" N VAL A 64 " pdb=" CA VAL A 64 " ideal model delta harmonic sigma weight residual 180.00 157.15 22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ASN C 63 " pdb=" C ASN C 63 " pdb=" N VAL C 64 " pdb=" CA VAL C 64 " ideal model delta harmonic sigma weight residual 180.00 157.24 22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA MET A 179 " pdb=" C MET A 179 " pdb=" N LEU A 180 " pdb=" CA LEU A 180 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 964 0.046 - 0.091: 419 0.091 - 0.137: 92 0.137 - 0.183: 21 0.183 - 0.228: 6 Chirality restraints: 1502 Sorted by residual: chirality pdb=" C1 NAG C 901 " pdb=" ND2 ASN C 309 " pdb=" C2 NAG C 901 " pdb=" O5 NAG C 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 309 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA TYR C 451 " pdb=" N TYR C 451 " pdb=" C TYR C 451 " pdb=" CB TYR C 451 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1499 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 320 " 0.096 2.00e-02 2.50e+03 4.85e-02 4.71e+01 pdb=" CG TYR C 320 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR C 320 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR C 320 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR C 320 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 320 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR C 320 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 320 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 320 " -0.096 2.00e-02 2.50e+03 4.85e-02 4.70e+01 pdb=" CG TYR A 320 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A 320 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR A 320 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 320 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 320 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 320 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 320 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 901 " -0.066 2.00e-02 2.50e+03 5.47e-02 3.74e+01 pdb=" C7 NAG A 901 " 0.004 2.00e-02 2.50e+03 pdb=" C8 NAG A 901 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG A 901 " 0.091 2.00e-02 2.50e+03 pdb=" O7 NAG A 901 " 0.017 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 4804 2.99 - 3.47: 10323 3.47 - 3.95: 16113 3.95 - 4.42: 19101 4.42 - 4.90: 29395 Nonbonded interactions: 79736 Sorted by model distance: nonbonded pdb=" O SER A 101 " pdb=" OG SER A 105 " model vdw 2.518 3.040 nonbonded pdb=" O SER C 101 " pdb=" OG SER C 105 " model vdw 2.519 3.040 nonbonded pdb=" OE2 GLU A 299 " pdb=" OG SER A 314 " model vdw 2.545 3.040 nonbonded pdb=" O ILE C 400 " pdb=" OG SER C 404 " model vdw 2.545 3.040 nonbonded pdb=" O ILE A 400 " pdb=" OG SER A 404 " model vdw 2.546 3.040 ... (remaining 79731 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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: 1.750 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.660 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 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 : 0.007 0.052 9094 Z= 0.467 Angle : 1.056 9.462 12356 Z= 0.603 Chirality : 0.053 0.228 1502 Planarity : 0.009 0.095 1476 Dihedral : 11.796 84.578 3210 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.71 (0.22), residues: 1110 helix: -0.36 (0.15), residues: 902 sheet: None (None), residues: 0 loop : -0.19 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.006 TRP A 100 HIS 0.007 0.003 HIS A 505 PHE 0.054 0.007 PHE A 694 TYR 0.096 0.009 TYR A 320 ARG 0.004 0.001 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.012 Fit side-chains REVERT: A 193 TRP cc_start: 0.6946 (t-100) cc_final: 0.6717 (t-100) outliers start: 0 outliers final: 1 residues processed: 202 average time/residue: 1.0010 time to fit residues: 218.7698 Evaluate side-chains 78 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 710 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 GLN ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 654 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9094 Z= 0.278 Angle : 0.692 8.469 12356 Z= 0.355 Chirality : 0.046 0.173 1502 Planarity : 0.005 0.034 1476 Dihedral : 4.933 34.849 1224 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.64 % Allowed : 10.16 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.88 (0.25), residues: 1110 helix: 1.51 (0.17), residues: 898 sheet: None (None), residues: 0 loop : 0.40 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 396 HIS 0.004 0.001 HIS A 310 PHE 0.022 0.002 PHE C 221 TYR 0.028 0.002 TYR C 455 ARG 0.006 0.001 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.7404 (ttm) cc_final: 0.7122 (ttm) REVERT: A 193 TRP cc_start: 0.7492 (t-100) cc_final: 0.7281 (t-100) outliers start: 26 outliers final: 3 residues processed: 132 average time/residue: 0.9645 time to fit residues: 139.5006 Evaluate side-chains 85 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 239 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 100 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 658 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9094 Z= 0.230 Angle : 0.615 10.343 12356 Z= 0.310 Chirality : 0.042 0.159 1502 Planarity : 0.004 0.036 1476 Dihedral : 4.587 31.551 1222 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.95 % Allowed : 10.37 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.25), residues: 1110 helix: 1.94 (0.17), residues: 898 sheet: None (None), residues: 0 loop : 0.84 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 193 HIS 0.003 0.001 HIS C 716 PHE 0.025 0.002 PHE C 221 TYR 0.029 0.002 TYR C 455 ARG 0.006 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.937 Fit side-chains REVERT: C 429 MET cc_start: 0.7079 (tpt) cc_final: 0.6790 (tpp) REVERT: A 37 MET cc_start: 0.7673 (ttm) cc_final: 0.7364 (ttm) REVERT: A 429 MET cc_start: 0.7085 (tpt) cc_final: 0.6817 (tpp) outliers start: 29 outliers final: 10 residues processed: 110 average time/residue: 1.0386 time to fit residues: 124.0263 Evaluate side-chains 79 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 389 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 0.0070 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 HIS C 658 HIS ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.7093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9094 Z= 0.280 Angle : 0.632 10.157 12356 Z= 0.319 Chirality : 0.043 0.158 1502 Planarity : 0.004 0.034 1476 Dihedral : 4.495 28.357 1222 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.74 % Allowed : 10.77 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.25), residues: 1110 helix: 1.92 (0.17), residues: 904 sheet: None (None), residues: 0 loop : 0.58 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 396 HIS 0.004 0.001 HIS A 716 PHE 0.024 0.002 PHE C 221 TYR 0.024 0.002 TYR A 455 ARG 0.003 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: C 37 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7657 (ttm) outliers start: 27 outliers final: 10 residues processed: 104 average time/residue: 0.8254 time to fit residues: 94.8690 Evaluate side-chains 93 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 401 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.7414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9094 Z= 0.237 Angle : 0.591 8.866 12356 Z= 0.297 Chirality : 0.042 0.204 1502 Planarity : 0.004 0.034 1476 Dihedral : 4.387 27.847 1222 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.35 % Allowed : 9.86 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.25), residues: 1110 helix: 2.11 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 0.65 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 363 HIS 0.004 0.001 HIS C 716 PHE 0.024 0.002 PHE A 221 TYR 0.023 0.002 TYR C 455 ARG 0.003 0.001 ARG C 295 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 402 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6817 (tt) REVERT: C 455 TYR cc_start: 0.7415 (m-80) cc_final: 0.7145 (m-80) REVERT: C 521 MET cc_start: 0.7544 (mmt) cc_final: 0.7250 (mmm) REVERT: A 402 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6907 (tt) outliers start: 33 outliers final: 10 residues processed: 113 average time/residue: 0.9631 time to fit residues: 118.6002 Evaluate side-chains 93 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 673 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.0030 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.7817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9094 Z= 0.304 Angle : 0.618 9.342 12356 Z= 0.312 Chirality : 0.043 0.195 1502 Planarity : 0.004 0.034 1476 Dihedral : 4.368 25.467 1222 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.15 % Allowed : 10.47 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.25), residues: 1110 helix: 2.01 (0.17), residues: 902 sheet: None (None), residues: 0 loop : 0.66 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 363 HIS 0.004 0.001 HIS A 716 PHE 0.025 0.002 PHE C 221 TYR 0.019 0.002 TYR C 451 ARG 0.002 0.000 ARG C 295 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 1.014 Fit side-chains REVERT: C 402 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6797 (tt) REVERT: C 521 MET cc_start: 0.7562 (mmt) cc_final: 0.7314 (mmm) REVERT: A 402 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.6971 (tt) outliers start: 31 outliers final: 12 residues processed: 102 average time/residue: 0.8909 time to fit residues: 100.5706 Evaluate side-chains 97 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.8056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9094 Z= 0.245 Angle : 0.606 9.978 12356 Z= 0.302 Chirality : 0.042 0.227 1502 Planarity : 0.004 0.033 1476 Dihedral : 4.298 24.454 1222 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.73 % Allowed : 12.60 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.25), residues: 1110 helix: 2.06 (0.17), residues: 896 sheet: None (None), residues: 0 loop : 0.63 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 460 HIS 0.004 0.001 HIS A 716 PHE 0.022 0.001 PHE C 221 TYR 0.020 0.002 TYR C 451 ARG 0.001 0.000 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.994 Fit side-chains REVERT: C 402 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6735 (tt) REVERT: C 455 TYR cc_start: 0.7380 (m-80) cc_final: 0.6849 (m-80) REVERT: C 521 MET cc_start: 0.7457 (mmt) cc_final: 0.7131 (mmm) REVERT: A 402 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7101 (tt) REVERT: A 430 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7230 (mtm) outliers start: 17 outliers final: 7 residues processed: 95 average time/residue: 0.9086 time to fit residues: 95.0458 Evaluate side-chains 95 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 430 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.8172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9094 Z= 0.195 Angle : 0.585 11.404 12356 Z= 0.294 Chirality : 0.041 0.227 1502 Planarity : 0.004 0.033 1476 Dihedral : 4.210 24.312 1222 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.93 % Allowed : 11.99 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.25), residues: 1110 helix: 2.14 (0.17), residues: 894 sheet: None (None), residues: 0 loop : 0.68 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 460 HIS 0.004 0.001 HIS A 716 PHE 0.020 0.001 PHE C 221 TYR 0.017 0.001 TYR C 451 ARG 0.001 0.000 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 1.001 Fit side-chains REVERT: C 402 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6630 (tt) REVERT: C 455 TYR cc_start: 0.7330 (m-80) cc_final: 0.6849 (m-80) REVERT: C 521 MET cc_start: 0.7414 (mmt) cc_final: 0.7102 (mmm) REVERT: A 402 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6865 (tt) REVERT: A 430 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.7166 (mtm) outliers start: 19 outliers final: 4 residues processed: 103 average time/residue: 0.8486 time to fit residues: 96.5831 Evaluate side-chains 88 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 430 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN C 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.8321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9094 Z= 0.243 Angle : 0.629 11.540 12356 Z= 0.310 Chirality : 0.042 0.248 1502 Planarity : 0.004 0.033 1476 Dihedral : 4.211 23.138 1222 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.63 % Allowed : 12.40 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.25), residues: 1110 helix: 2.12 (0.17), residues: 898 sheet: None (None), residues: 0 loop : 0.73 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 460 HIS 0.004 0.001 HIS C 716 PHE 0.021 0.002 PHE A 221 TYR 0.018 0.001 TYR C 451 ARG 0.002 0.000 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.956 Fit side-chains REVERT: C 402 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6631 (tt) REVERT: C 455 TYR cc_start: 0.7235 (m-80) cc_final: 0.6843 (m-80) REVERT: C 521 MET cc_start: 0.7367 (mmt) cc_final: 0.7078 (mmm) REVERT: A 402 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6759 (tt) REVERT: A 666 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7385 (mt) outliers start: 16 outliers final: 5 residues processed: 96 average time/residue: 0.9463 time to fit residues: 99.7148 Evaluate side-chains 93 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 666 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 102 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.8423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9094 Z= 0.228 Angle : 0.627 11.710 12356 Z= 0.311 Chirality : 0.042 0.334 1502 Planarity : 0.004 0.033 1476 Dihedral : 4.164 22.026 1222 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.91 % Allowed : 13.52 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.25), residues: 1110 helix: 2.12 (0.17), residues: 900 sheet: None (None), residues: 0 loop : 0.64 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 460 HIS 0.004 0.001 HIS A 716 PHE 0.021 0.001 PHE A 221 TYR 0.018 0.001 TYR C 451 ARG 0.001 0.000 ARG C 295 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 1.059 Fit side-chains REVERT: C 402 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6515 (tt) REVERT: C 455 TYR cc_start: 0.7057 (m-80) cc_final: 0.6634 (m-80) REVERT: C 666 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7604 (mt) REVERT: A 402 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6752 (tt) outliers start: 9 outliers final: 5 residues processed: 89 average time/residue: 1.0047 time to fit residues: 97.6961 Evaluate side-chains 84 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 666 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.129953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.094265 restraints weight = 16868.162| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.29 r_work: 0.3318 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.8538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9094 Z= 0.229 Angle : 0.643 11.586 12356 Z= 0.314 Chirality : 0.042 0.352 1502 Planarity : 0.004 0.033 1476 Dihedral : 4.146 21.072 1222 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.52 % Allowed : 12.80 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.25), residues: 1110 helix: 2.13 (0.17), residues: 900 sheet: None (None), residues: 0 loop : 0.63 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 460 HIS 0.004 0.001 HIS C 716 PHE 0.020 0.001 PHE A 221 TYR 0.018 0.001 TYR C 451 ARG 0.002 0.000 ARG C 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2887.48 seconds wall clock time: 52 minutes 58.61 seconds (3178.61 seconds total)