Starting phenix.real_space_refine on Wed Sep 25 01:44:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/09_2024/8exq_28659.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/09_2024/8exq_28659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/09_2024/8exq_28659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/09_2024/8exq_28659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/09_2024/8exq_28659.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/09_2024/8exq_28659.cif" } resolution = 4.9 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= 0.003 sd= 0.045 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 38 5.16 5 C 6112 2.51 5 N 1534 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9304 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4651 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 11, 'TRANS': 542} Chain breaks: 1 Chain: "A" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4651 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 11, 'TRANS': 542} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.27, per 1000 atoms: 0.57 Number of scatterers: 9304 At special positions: 0 Unit cell: (73.9927, 108.282, 135.353, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 38 16.00 O 1618 8.00 N 1534 7.00 C 6112 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 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 201 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 205 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 201 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 205 " 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 57.5% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'B' and resid 2 through 31 Processing helix chain 'B' and resid 35 through 38 Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 99 through 133 removed outlier: 3.571A pdb=" N ASP B 103 " --> pdb=" O TRP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 194 through 208 Processing helix chain 'B' and resid 209 through 224 Processing helix chain 'B' and resid 229 through 251 removed outlier: 3.969A pdb=" N ARG B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 253 No H-bonds generated for 'chain 'B' and resid 252 through 253' Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 257 through 268 removed outlier: 3.647A pdb=" N SER B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 308 through 327 Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 390 through 402 removed outlier: 4.270A pdb=" N TYR B 394 " --> pdb=" O THR B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 483 through 497 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 564 through 579 Processing helix chain 'A' and resid 2 through 31 Processing helix chain 'A' and resid 35 through 38 Processing helix chain 'A' and resid 39 through 46 removed outlier: 3.563A pdb=" N LEU A 43 " --> pdb=" O TRP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 99 through 132 Processing helix chain 'A' and resid 139 through 152 removed outlier: 4.659A pdb=" N ASN A 152 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 209 through 224 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.620A pdb=" N ASN A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 removed outlier: 5.426A pdb=" N ASN A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 257 through 272 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 308 through 327 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 390 through 402 removed outlier: 4.455A pdb=" N TYR A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 483 through 497 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 564 through 579 Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.686A pdb=" N PHE B 90 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE A 531 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR B 92 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 532 " --> pdb=" O TYR A 536 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASP A 346 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE A 375 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN A 348 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.686A pdb=" N PHE B 90 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE A 531 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR B 92 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLY A 525 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU A 514 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 164 removed outlier: 6.457A pdb=" N VAL B 160 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE B 182 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG B 162 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.693A pdb=" N ASP B 346 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE B 375 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN B 348 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 532 " --> pdb=" O TYR B 536 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY B 525 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU B 514 " --> pdb=" O GLY B 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.693A pdb=" N ASP B 346 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE B 375 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN B 348 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 532 " --> pdb=" O TYR B 536 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N THR A 92 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR B 529 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE A 94 " --> pdb=" O THR B 529 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 531 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 136 through 137 538 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2085 1.32 - 1.46: 3022 1.46 - 1.59: 4346 1.59 - 1.73: 11 1.73 - 1.86: 68 Bond restraints: 9532 Sorted by residual: bond pdb=" CB HIS B 201 " pdb=" CG HIS B 201 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.14e+01 bond pdb=" CB HIS B 153 " pdb=" CG HIS B 153 " ideal model delta sigma weight residual 1.497 1.418 0.079 1.40e-02 5.10e+03 3.22e+01 bond pdb=" CB TYR B 552 " pdb=" CG TYR B 552 " ideal model delta sigma weight residual 1.512 1.397 0.115 2.20e-02 2.07e+03 2.75e+01 bond pdb=" CB PHE A 90 " pdb=" CG PHE A 90 " ideal model delta sigma weight residual 1.502 1.385 0.117 2.30e-02 1.89e+03 2.58e+01 bond pdb=" CG MET B 494 " pdb=" SD MET B 494 " ideal model delta sigma weight residual 1.803 1.678 0.125 2.50e-02 1.60e+03 2.52e+01 ... (remaining 9527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 10461 2.06 - 4.11: 1944 4.11 - 6.17: 331 6.17 - 8.22: 79 8.22 - 10.28: 21 Bond angle restraints: 12836 Sorted by residual: angle pdb=" CA PHE A 313 " pdb=" CB PHE A 313 " pdb=" CG PHE A 313 " ideal model delta sigma weight residual 113.80 105.83 7.97 1.00e+00 1.00e+00 6.36e+01 angle pdb=" CA ASP A 550 " pdb=" CB ASP A 550 " pdb=" CG ASP A 550 " ideal model delta sigma weight residual 112.60 120.57 -7.97 1.00e+00 1.00e+00 6.36e+01 angle pdb=" C SER B 386 " pdb=" N PRO B 387 " pdb=" CA PRO B 387 " ideal model delta sigma weight residual 119.56 127.47 -7.91 1.01e+00 9.80e-01 6.13e+01 angle pdb=" C TYR B 419 " pdb=" N PRO B 420 " pdb=" CA PRO B 420 " ideal model delta sigma weight residual 119.56 127.53 -7.97 1.02e+00 9.61e-01 6.11e+01 angle pdb=" C TYR A 419 " pdb=" N PRO A 420 " pdb=" CA PRO A 420 " ideal model delta sigma weight residual 119.56 127.44 -7.88 1.02e+00 9.61e-01 5.96e+01 ... (remaining 12831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5476 17.91 - 35.81: 176 35.81 - 53.72: 26 53.72 - 71.62: 9 71.62 - 89.53: 7 Dihedral angle restraints: 5694 sinusoidal: 2374 harmonic: 3320 Sorted by residual: dihedral pdb=" C ILE B 48 " pdb=" N ILE B 48 " pdb=" CA ILE B 48 " pdb=" CB ILE B 48 " ideal model delta harmonic sigma weight residual -122.00 -131.80 9.80 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" C PHE B 501 " pdb=" N PHE B 501 " pdb=" CA PHE B 501 " pdb=" CB PHE B 501 " ideal model delta harmonic sigma weight residual -122.60 -113.60 -9.00 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" C TYR B 385 " pdb=" N TYR B 385 " pdb=" CA TYR B 385 " pdb=" CB TYR B 385 " ideal model delta harmonic sigma weight residual -122.60 -113.89 -8.71 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 5691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 923 0.095 - 0.189: 364 0.189 - 0.284: 87 0.284 - 0.379: 13 0.379 - 0.473: 1 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CB ILE B 531 " pdb=" CA ILE B 531 " pdb=" CG1 ILE B 531 " pdb=" CG2 ILE B 531 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CA PHE A 313 " pdb=" N PHE A 313 " pdb=" C PHE A 313 " pdb=" CB PHE A 313 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA ASN B 436 " pdb=" N ASN B 436 " pdb=" C ASN B 436 " pdb=" CB ASN B 436 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 1385 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 36 " -0.077 2.00e-02 2.50e+03 4.24e-02 3.60e+01 pdb=" CG TYR A 36 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 36 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 36 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 36 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 36 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 36 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 36 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 540 " -0.075 2.00e-02 2.50e+03 3.64e-02 3.32e+01 pdb=" CG TRP A 540 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 540 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 540 " 0.030 2.00e-02 2.50e+03 pdb=" NE1 TRP A 540 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 540 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 540 " 0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 540 " -0.048 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 540 " 0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP A 540 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 373 " 0.064 2.00e-02 2.50e+03 3.95e-02 3.12e+01 pdb=" CG TYR B 373 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 373 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR B 373 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR B 373 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR B 373 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR B 373 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 373 " 0.068 2.00e-02 2.50e+03 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 67 2.58 - 3.16: 8618 3.16 - 3.74: 15153 3.74 - 4.32: 22622 4.32 - 4.90: 34188 Nonbonded interactions: 80648 Sorted by model distance: nonbonded pdb=" OE1 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.002 2.230 nonbonded pdb=" OE2 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.033 2.230 nonbonded pdb=" OE2 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.044 2.230 nonbonded pdb=" OE1 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.061 2.230 nonbonded pdb=" CD GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.345 2.460 ... (remaining 80643 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 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.540 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4707 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 : 0.020 0.130 9532 Z= 1.264 Angle : 1.739 10.276 12836 Z= 1.191 Chirality : 0.104 0.473 1388 Planarity : 0.009 0.044 1574 Dihedral : 10.285 89.529 3554 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.55 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.24), residues: 1100 helix: 0.79 (0.20), residues: 534 sheet: -0.15 (0.46), residues: 117 loop : -0.21 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.013 TRP A 540 HIS 0.009 0.002 HIS A 153 PHE 0.037 0.007 PHE A 274 TYR 0.077 0.012 TYR A 36 ARG 0.007 0.001 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8886 (t80) cc_final: 0.7920 (t80) REVERT: A 131 LEU cc_start: 0.9043 (mt) cc_final: 0.8838 (mp) REVERT: A 143 LYS cc_start: 0.8863 (tttm) cc_final: 0.8445 (tmtt) REVERT: A 147 ASP cc_start: 0.8624 (m-30) cc_final: 0.8340 (m-30) REVERT: A 149 ILE cc_start: 0.9315 (mt) cc_final: 0.8812 (mm) REVERT: A 180 ILE cc_start: 0.8271 (mt) cc_final: 0.7615 (mt) REVERT: A 181 LEU cc_start: 0.9043 (mp) cc_final: 0.8751 (mp) REVERT: A 208 ASN cc_start: 0.9097 (m-40) cc_final: 0.7563 (m110) REVERT: A 215 ILE cc_start: 0.8958 (mt) cc_final: 0.8726 (mt) REVERT: A 216 ILE cc_start: 0.9672 (mt) cc_final: 0.9248 (mt) REVERT: A 220 PHE cc_start: 0.7931 (m-10) cc_final: 0.7512 (m-80) REVERT: A 227 ASN cc_start: 0.8976 (t0) cc_final: 0.8402 (t0) REVERT: A 248 PHE cc_start: 0.6596 (m-80) cc_final: 0.6072 (m-80) REVERT: A 292 LYS cc_start: 0.8466 (tptt) cc_final: 0.7860 (tttm) REVERT: A 296 ILE cc_start: 0.9503 (mt) cc_final: 0.9228 (mm) REVERT: A 297 ASN cc_start: 0.8594 (m-40) cc_final: 0.8230 (m110) REVERT: A 311 LEU cc_start: 0.9239 (pp) cc_final: 0.8840 (mp) REVERT: A 368 MET cc_start: -0.2061 (tpt) cc_final: -0.2607 (ttm) REVERT: A 462 ASN cc_start: 0.5872 (t0) cc_final: 0.5219 (m-40) REVERT: A 553 TYR cc_start: 0.3296 (m-80) cc_final: 0.1548 (m-80) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1827 time to fit residues: 43.7459 Evaluate side-chains 114 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 0.0040 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 30.0000 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 overall best weight: 1.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 241 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4532 moved from start: 1.0546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9532 Z= 0.261 Angle : 0.774 9.122 12836 Z= 0.431 Chirality : 0.048 0.156 1388 Planarity : 0.005 0.042 1574 Dihedral : 5.727 29.939 1208 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.77 % Allowed : 3.47 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1100 helix: 1.28 (0.21), residues: 562 sheet: 0.24 (0.46), residues: 126 loop : -0.78 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 414 HIS 0.009 0.002 HIS B 213 PHE 0.035 0.003 PHE A 14 TYR 0.030 0.002 TYR B 524 ARG 0.003 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 157 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8654 (pttp) cc_final: 0.7915 (pttt) REVERT: A 31 ASN cc_start: 0.8775 (m-40) cc_final: 0.8117 (p0) REVERT: A 110 TRP cc_start: 0.7486 (t60) cc_final: 0.7051 (t60) REVERT: A 126 LEU cc_start: 0.9292 (mt) cc_final: 0.8911 (mt) REVERT: A 127 TYR cc_start: 0.7685 (t80) cc_final: 0.7105 (t80) REVERT: A 130 TYR cc_start: 0.7867 (m-10) cc_final: 0.7657 (m-80) REVERT: A 208 ASN cc_start: 0.8689 (m-40) cc_final: 0.7623 (m110) REVERT: A 227 ASN cc_start: 0.8554 (t0) cc_final: 0.8263 (t0) REVERT: A 244 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7428 (mm-30) REVERT: A 295 LEU cc_start: 0.9316 (mt) cc_final: 0.8855 (mt) REVERT: A 320 LEU cc_start: 0.9288 (mt) cc_final: 0.9027 (mt) REVERT: A 365 MET cc_start: 0.1016 (tmm) cc_final: 0.0481 (tpp) REVERT: A 368 MET cc_start: -0.0866 (tpt) cc_final: -0.1323 (ttm) REVERT: A 462 ASN cc_start: 0.5132 (t0) cc_final: 0.4449 (m-40) outliers start: 4 outliers final: 1 residues processed: 159 average time/residue: 0.1664 time to fit residues: 33.1835 Evaluate side-chains 124 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 9.9990 chunk 31 optimal weight: 0.0970 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.0470 chunk 100 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 overall best weight: 0.5876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 282 HIS A 500 HIS A 557 HIS A 567 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4543 moved from start: 1.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9532 Z= 0.199 Angle : 0.680 10.019 12836 Z= 0.373 Chirality : 0.043 0.151 1388 Planarity : 0.004 0.042 1574 Dihedral : 5.318 25.958 1208 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.19 % Allowed : 3.09 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1100 helix: 0.72 (0.21), residues: 564 sheet: -0.19 (0.43), residues: 126 loop : -1.02 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 414 HIS 0.003 0.001 HIS A 213 PHE 0.042 0.002 PHE B 14 TYR 0.020 0.002 TYR B 524 ARG 0.002 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 TRP cc_start: 0.7511 (t60) cc_final: 0.7098 (t60) REVERT: A 121 PHE cc_start: 0.8338 (t80) cc_final: 0.7656 (t80) REVERT: A 126 LEU cc_start: 0.9170 (mt) cc_final: 0.8494 (mt) REVERT: A 127 TYR cc_start: 0.7877 (t80) cc_final: 0.6895 (t80) REVERT: A 130 TYR cc_start: 0.7676 (m-10) cc_final: 0.7443 (m-80) REVERT: A 198 ILE cc_start: 0.8805 (pt) cc_final: 0.8296 (pt) REVERT: A 199 ILE cc_start: 0.9391 (mm) cc_final: 0.9012 (mm) REVERT: A 208 ASN cc_start: 0.8578 (m-40) cc_final: 0.7558 (p0) REVERT: A 213 HIS cc_start: 0.8400 (m90) cc_final: 0.8113 (m90) REVERT: A 227 ASN cc_start: 0.8481 (t0) cc_final: 0.7982 (t0) REVERT: A 233 VAL cc_start: 0.8918 (m) cc_final: 0.8679 (m) REVERT: A 295 LEU cc_start: 0.9212 (mt) cc_final: 0.8767 (mt) REVERT: A 297 ASN cc_start: 0.8336 (m-40) cc_final: 0.8128 (m-40) REVERT: A 302 ASN cc_start: 0.8334 (t0) cc_final: 0.7838 (t0) REVERT: A 317 PHE cc_start: 0.8881 (m-80) cc_final: 0.8524 (m-80) REVERT: A 322 MET cc_start: 0.9246 (mpp) cc_final: 0.9036 (mmt) REVERT: A 365 MET cc_start: 0.0682 (tmm) cc_final: -0.1174 (tpp) REVERT: A 368 MET cc_start: -0.1010 (tpt) cc_final: -0.1553 (ttp) REVERT: A 414 TRP cc_start: 0.4109 (t60) cc_final: 0.3785 (t60) REVERT: A 495 MET cc_start: 0.4669 (mmt) cc_final: 0.4222 (mmm) outliers start: 1 outliers final: 1 residues processed: 152 average time/residue: 0.1756 time to fit residues: 33.2616 Evaluate side-chains 120 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.3980 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 0.5980 chunk 52 optimal weight: 0.3980 chunk 95 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4540 moved from start: 1.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9532 Z= 0.177 Angle : 0.656 7.045 12836 Z= 0.365 Chirality : 0.042 0.138 1388 Planarity : 0.004 0.038 1574 Dihedral : 4.929 19.166 1208 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1100 helix: 0.59 (0.21), residues: 566 sheet: -0.10 (0.41), residues: 136 loop : -1.38 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 414 HIS 0.007 0.001 HIS A 201 PHE 0.044 0.002 PHE B 14 TYR 0.024 0.002 TYR A 544 ARG 0.007 0.001 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7827 (tpt90) cc_final: 0.7335 (tpt90) REVERT: A 110 TRP cc_start: 0.7410 (t60) cc_final: 0.6933 (t60) REVERT: A 121 PHE cc_start: 0.8397 (t80) cc_final: 0.8091 (t80) REVERT: A 122 LEU cc_start: 0.9257 (tp) cc_final: 0.8887 (tp) REVERT: A 126 LEU cc_start: 0.9093 (mt) cc_final: 0.8652 (mt) REVERT: A 130 TYR cc_start: 0.7754 (m-10) cc_final: 0.7503 (m-80) REVERT: A 141 ASN cc_start: 0.8871 (m-40) cc_final: 0.8509 (m-40) REVERT: A 198 ILE cc_start: 0.9008 (pt) cc_final: 0.8416 (pt) REVERT: A 199 ILE cc_start: 0.9454 (mm) cc_final: 0.9031 (mm) REVERT: A 202 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8121 (mt-10) REVERT: A 208 ASN cc_start: 0.9082 (m-40) cc_final: 0.8027 (m110) REVERT: A 215 ILE cc_start: 0.8488 (tp) cc_final: 0.8168 (pt) REVERT: A 227 ASN cc_start: 0.8488 (t0) cc_final: 0.7811 (t0) REVERT: A 233 VAL cc_start: 0.8886 (m) cc_final: 0.8670 (m) REVERT: A 237 ILE cc_start: 0.9283 (mt) cc_final: 0.8981 (mt) REVERT: A 240 ASP cc_start: 0.8664 (m-30) cc_final: 0.8432 (m-30) REVERT: A 244 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7519 (mm-30) REVERT: A 248 PHE cc_start: 0.6425 (m-10) cc_final: 0.6068 (m-10) REVERT: A 295 LEU cc_start: 0.9167 (mt) cc_final: 0.8776 (mt) REVERT: A 302 ASN cc_start: 0.7967 (t0) cc_final: 0.7724 (t0) REVERT: A 317 PHE cc_start: 0.8808 (m-80) cc_final: 0.8481 (m-80) REVERT: A 365 MET cc_start: 0.0963 (tmm) cc_final: -0.0963 (tpp) REVERT: A 368 MET cc_start: -0.0064 (tpt) cc_final: -0.2599 (mtp) REVERT: A 414 TRP cc_start: 0.4196 (t60) cc_final: 0.3862 (t60) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1512 time to fit residues: 28.4316 Evaluate side-chains 115 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 0.0040 chunk 43 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS A 239 HIS A 567 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4528 moved from start: 1.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9532 Z= 0.169 Angle : 0.614 5.839 12836 Z= 0.346 Chirality : 0.041 0.147 1388 Planarity : 0.004 0.034 1574 Dihedral : 4.779 17.361 1208 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1100 helix: 0.36 (0.20), residues: 568 sheet: 0.01 (0.42), residues: 136 loop : -1.37 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 424 HIS 0.006 0.001 HIS A 231 PHE 0.041 0.002 PHE B 22 TYR 0.018 0.001 TYR A 544 ARG 0.007 0.001 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.8484 (pt) cc_final: 0.8198 (pt) REVERT: A 110 TRP cc_start: 0.7391 (t60) cc_final: 0.6977 (t60) REVERT: A 121 PHE cc_start: 0.8507 (t80) cc_final: 0.8034 (t80) REVERT: A 122 LEU cc_start: 0.9202 (tp) cc_final: 0.8831 (tp) REVERT: A 126 LEU cc_start: 0.9134 (mt) cc_final: 0.8643 (mt) REVERT: A 130 TYR cc_start: 0.8011 (m-10) cc_final: 0.7724 (m-80) REVERT: A 141 ASN cc_start: 0.8755 (m-40) cc_final: 0.8176 (p0) REVERT: A 145 LYS cc_start: 0.9551 (mttm) cc_final: 0.9295 (mttm) REVERT: A 153 HIS cc_start: 0.7461 (m90) cc_final: 0.7101 (m90) REVERT: A 178 TYR cc_start: 0.6164 (m-80) cc_final: 0.5044 (m-80) REVERT: A 180 ILE cc_start: 0.8700 (mp) cc_final: 0.7433 (mp) REVERT: A 208 ASN cc_start: 0.9015 (m-40) cc_final: 0.8468 (m110) REVERT: A 215 ILE cc_start: 0.8673 (tp) cc_final: 0.8441 (pt) REVERT: A 222 ILE cc_start: 0.9208 (pt) cc_final: 0.8989 (pt) REVERT: A 227 ASN cc_start: 0.8490 (t0) cc_final: 0.7802 (t0) REVERT: A 233 VAL cc_start: 0.8853 (m) cc_final: 0.8604 (m) REVERT: A 239 HIS cc_start: 0.8300 (m90) cc_final: 0.7953 (m90) REVERT: A 267 ASP cc_start: 0.8305 (m-30) cc_final: 0.7766 (m-30) REVERT: A 295 LEU cc_start: 0.9202 (mt) cc_final: 0.8933 (mt) REVERT: A 302 ASN cc_start: 0.8090 (t0) cc_final: 0.7818 (t0) REVERT: A 365 MET cc_start: 0.1182 (tmm) cc_final: -0.0642 (tpp) REVERT: A 368 MET cc_start: 0.0094 (tpt) cc_final: -0.1483 (mtp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1452 time to fit residues: 26.5425 Evaluate side-chains 115 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 0.0770 chunk 88 optimal weight: 0.3980 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4569 moved from start: 1.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9532 Z= 0.175 Angle : 0.630 8.612 12836 Z= 0.350 Chirality : 0.041 0.140 1388 Planarity : 0.004 0.033 1574 Dihedral : 4.687 19.282 1208 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.24), residues: 1100 helix: 0.33 (0.20), residues: 566 sheet: 0.22 (0.43), residues: 136 loop : -1.29 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 414 HIS 0.009 0.001 HIS A 418 PHE 0.062 0.002 PHE B 14 TYR 0.018 0.001 TYR B 544 ARG 0.005 0.001 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.8522 (pt) cc_final: 0.8168 (pt) REVERT: A 39 TRP cc_start: 0.7900 (m100) cc_final: 0.7081 (m-90) REVERT: A 110 TRP cc_start: 0.7447 (t60) cc_final: 0.7006 (t60) REVERT: A 121 PHE cc_start: 0.8480 (t80) cc_final: 0.8209 (t80) REVERT: A 122 LEU cc_start: 0.9329 (tp) cc_final: 0.9022 (tp) REVERT: A 126 LEU cc_start: 0.9021 (mt) cc_final: 0.8304 (mt) REVERT: A 130 TYR cc_start: 0.8086 (m-10) cc_final: 0.7772 (m-80) REVERT: A 138 LEU cc_start: 0.7014 (mt) cc_final: 0.6757 (mt) REVERT: A 141 ASN cc_start: 0.8940 (m-40) cc_final: 0.8538 (p0) REVERT: A 178 TYR cc_start: 0.5600 (m-80) cc_final: 0.4732 (m-80) REVERT: A 198 ILE cc_start: 0.9183 (pt) cc_final: 0.8593 (pt) REVERT: A 199 ILE cc_start: 0.9541 (mm) cc_final: 0.9109 (mm) REVERT: A 208 ASN cc_start: 0.8886 (m-40) cc_final: 0.8250 (m110) REVERT: A 215 ILE cc_start: 0.8651 (tp) cc_final: 0.8421 (pt) REVERT: A 222 ILE cc_start: 0.9216 (pt) cc_final: 0.8989 (pt) REVERT: A 233 VAL cc_start: 0.8858 (m) cc_final: 0.8627 (m) REVERT: A 267 ASP cc_start: 0.8266 (m-30) cc_final: 0.7620 (m-30) REVERT: A 295 LEU cc_start: 0.9219 (mt) cc_final: 0.8947 (mt) REVERT: A 302 ASN cc_start: 0.8086 (t0) cc_final: 0.7797 (t0) REVERT: A 313 PHE cc_start: 0.9028 (m-10) cc_final: 0.8514 (m-80) REVERT: A 317 PHE cc_start: 0.8969 (m-80) cc_final: 0.8138 (m-80) REVERT: A 320 LEU cc_start: 0.9360 (mm) cc_final: 0.8946 (mm) REVERT: A 322 MET cc_start: 0.9373 (mpp) cc_final: 0.9118 (mpp) REVERT: A 365 MET cc_start: 0.1107 (tmm) cc_final: 0.0882 (tpp) REVERT: A 368 MET cc_start: -0.0212 (tpt) cc_final: -0.0719 (ttm) REVERT: A 579 MET cc_start: -0.0308 (tpt) cc_final: -0.0926 (ttt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1404 time to fit residues: 25.1925 Evaluate side-chains 112 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 89 optimal weight: 0.0870 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.0470 chunk 65 optimal weight: 0.0370 chunk 42 optimal weight: 1.9990 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4550 moved from start: 1.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9532 Z= 0.155 Angle : 0.608 6.497 12836 Z= 0.340 Chirality : 0.042 0.170 1388 Planarity : 0.003 0.038 1574 Dihedral : 4.495 16.309 1208 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1100 helix: 0.47 (0.20), residues: 570 sheet: 0.03 (0.43), residues: 136 loop : -1.35 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 414 HIS 0.004 0.001 HIS B 201 PHE 0.026 0.002 PHE B 14 TYR 0.018 0.001 TYR A 203 ARG 0.005 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.8604 (pt) cc_final: 0.8140 (pt) REVERT: A 39 TRP cc_start: 0.7852 (m100) cc_final: 0.7201 (m-90) REVERT: A 110 TRP cc_start: 0.7483 (t60) cc_final: 0.7065 (t60) REVERT: A 122 LEU cc_start: 0.9189 (tp) cc_final: 0.8706 (tp) REVERT: A 126 LEU cc_start: 0.8969 (mt) cc_final: 0.8254 (mt) REVERT: A 130 TYR cc_start: 0.8076 (m-10) cc_final: 0.7859 (m-80) REVERT: A 138 LEU cc_start: 0.7092 (mt) cc_final: 0.6608 (mt) REVERT: A 141 ASN cc_start: 0.8826 (m-40) cc_final: 0.8337 (p0) REVERT: A 172 THR cc_start: 0.8417 (m) cc_final: 0.8066 (m) REVERT: A 178 TYR cc_start: 0.5487 (m-80) cc_final: 0.4774 (m-80) REVERT: A 198 ILE cc_start: 0.9192 (pt) cc_final: 0.8556 (pt) REVERT: A 199 ILE cc_start: 0.9519 (mm) cc_final: 0.9114 (mm) REVERT: A 213 HIS cc_start: 0.8008 (m90) cc_final: 0.7773 (m170) REVERT: A 233 VAL cc_start: 0.8859 (m) cc_final: 0.8627 (m) REVERT: A 248 PHE cc_start: 0.6236 (m-10) cc_final: 0.5977 (m-10) REVERT: A 267 ASP cc_start: 0.8197 (m-30) cc_final: 0.7547 (m-30) REVERT: A 291 LEU cc_start: 0.8111 (tp) cc_final: 0.7502 (tp) REVERT: A 295 LEU cc_start: 0.9189 (mt) cc_final: 0.8764 (mt) REVERT: A 302 ASN cc_start: 0.8102 (t0) cc_final: 0.7872 (t0) REVERT: A 313 PHE cc_start: 0.8979 (m-10) cc_final: 0.8565 (m-80) REVERT: A 317 PHE cc_start: 0.8892 (m-80) cc_final: 0.8318 (m-80) REVERT: A 320 LEU cc_start: 0.9303 (mm) cc_final: 0.8892 (mm) REVERT: A 365 MET cc_start: 0.1025 (tmm) cc_final: 0.0795 (tpp) REVERT: A 368 MET cc_start: 0.0007 (tpt) cc_final: -0.1318 (mtp) REVERT: A 554 PHE cc_start: 0.3503 (p90) cc_final: 0.3126 (p90) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1320 time to fit residues: 23.7563 Evaluate side-chains 113 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4567 moved from start: 1.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9532 Z= 0.165 Angle : 0.636 9.466 12836 Z= 0.345 Chirality : 0.042 0.157 1388 Planarity : 0.004 0.040 1574 Dihedral : 4.487 17.151 1208 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1100 helix: 0.49 (0.20), residues: 574 sheet: 0.07 (0.43), residues: 136 loop : -1.39 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 414 HIS 0.004 0.001 HIS A 201 PHE 0.023 0.002 PHE B 16 TYR 0.017 0.001 TYR A 544 ARG 0.005 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LEU cc_start: 0.9369 (tp) cc_final: 0.9123 (tp) REVERT: A 12 PHE cc_start: 0.8066 (t80) cc_final: 0.7686 (t80) REVERT: A 20 LEU cc_start: 0.9385 (mt) cc_final: 0.8661 (mt) REVERT: A 25 ILE cc_start: 0.8615 (pt) cc_final: 0.8157 (pt) REVERT: A 39 TRP cc_start: 0.7855 (m100) cc_final: 0.7251 (m-90) REVERT: A 110 TRP cc_start: 0.7441 (t60) cc_final: 0.7103 (t60) REVERT: A 122 LEU cc_start: 0.9196 (tp) cc_final: 0.8799 (tt) REVERT: A 126 LEU cc_start: 0.8926 (mt) cc_final: 0.8247 (mt) REVERT: A 130 TYR cc_start: 0.8305 (m-10) cc_final: 0.7925 (m-80) REVERT: A 138 LEU cc_start: 0.6522 (mt) cc_final: 0.6030 (mt) REVERT: A 178 TYR cc_start: 0.5597 (m-80) cc_final: 0.4948 (m-80) REVERT: A 198 ILE cc_start: 0.9231 (pt) cc_final: 0.8590 (pt) REVERT: A 199 ILE cc_start: 0.9544 (mm) cc_final: 0.9046 (mm) REVERT: A 208 ASN cc_start: 0.8672 (m-40) cc_final: 0.8007 (m110) REVERT: A 233 VAL cc_start: 0.8873 (m) cc_final: 0.8625 (m) REVERT: A 248 PHE cc_start: 0.6243 (m-10) cc_final: 0.5949 (m-10) REVERT: A 267 ASP cc_start: 0.8191 (m-30) cc_final: 0.7529 (m-30) REVERT: A 295 LEU cc_start: 0.9200 (mt) cc_final: 0.8934 (mt) REVERT: A 302 ASN cc_start: 0.8153 (t0) cc_final: 0.7854 (t0) REVERT: A 313 PHE cc_start: 0.8962 (m-10) cc_final: 0.8486 (m-80) REVERT: A 317 PHE cc_start: 0.8946 (m-80) cc_final: 0.8357 (m-80) REVERT: A 320 LEU cc_start: 0.9310 (mm) cc_final: 0.8949 (mm) REVERT: A 365 MET cc_start: 0.0543 (tmm) cc_final: -0.0653 (tpp) REVERT: A 368 MET cc_start: -0.0147 (tpt) cc_final: -0.1495 (mtp) REVERT: A 554 PHE cc_start: 0.3349 (p90) cc_final: 0.3119 (p90) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1463 time to fit residues: 26.2647 Evaluate side-chains 104 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A 213 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4558 moved from start: 1.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9532 Z= 0.165 Angle : 0.632 8.638 12836 Z= 0.347 Chirality : 0.043 0.166 1388 Planarity : 0.005 0.084 1574 Dihedral : 4.558 20.310 1208 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.24), residues: 1100 helix: 0.58 (0.20), residues: 570 sheet: -0.16 (0.43), residues: 136 loop : -1.50 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 414 HIS 0.004 0.001 HIS B 213 PHE 0.039 0.002 PHE A 14 TYR 0.016 0.001 TYR B 441 ARG 0.010 0.001 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LEU cc_start: 0.9515 (tp) cc_final: 0.9308 (tp) REVERT: A 12 PHE cc_start: 0.7937 (t80) cc_final: 0.7655 (t80) REVERT: A 39 TRP cc_start: 0.7750 (m100) cc_final: 0.7258 (m-90) REVERT: A 110 TRP cc_start: 0.7447 (t60) cc_final: 0.7088 (t60) REVERT: A 122 LEU cc_start: 0.9216 (tp) cc_final: 0.8810 (tp) REVERT: A 126 LEU cc_start: 0.9061 (mt) cc_final: 0.8368 (mt) REVERT: A 130 TYR cc_start: 0.8432 (m-10) cc_final: 0.7923 (m-80) REVERT: A 138 LEU cc_start: 0.5944 (mt) cc_final: 0.5626 (mt) REVERT: A 142 GLU cc_start: 0.8430 (pp20) cc_final: 0.8177 (pp20) REVERT: A 172 THR cc_start: 0.8439 (m) cc_final: 0.7971 (m) REVERT: A 178 TYR cc_start: 0.5512 (m-80) cc_final: 0.4943 (m-80) REVERT: A 198 ILE cc_start: 0.9245 (pt) cc_final: 0.8610 (pt) REVERT: A 199 ILE cc_start: 0.9549 (mm) cc_final: 0.9079 (mm) REVERT: A 208 ASN cc_start: 0.8884 (m-40) cc_final: 0.8280 (m110) REVERT: A 213 HIS cc_start: 0.8052 (m90) cc_final: 0.7816 (m170) REVERT: A 218 ASN cc_start: 0.8705 (t0) cc_final: 0.8060 (t0) REVERT: A 233 VAL cc_start: 0.8894 (m) cc_final: 0.8654 (m) REVERT: A 248 PHE cc_start: 0.6288 (m-10) cc_final: 0.5886 (m-10) REVERT: A 295 LEU cc_start: 0.9237 (mt) cc_final: 0.8942 (mt) REVERT: A 302 ASN cc_start: 0.7411 (t0) cc_final: 0.7020 (t0) REVERT: A 313 PHE cc_start: 0.9004 (m-10) cc_final: 0.8695 (m-80) REVERT: A 317 PHE cc_start: 0.8768 (m-80) cc_final: 0.8214 (m-80) REVERT: A 365 MET cc_start: 0.1182 (tmm) cc_final: -0.0371 (tpp) REVERT: A 368 MET cc_start: 0.0010 (tpt) cc_final: -0.1294 (mtp) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1591 time to fit residues: 26.2833 Evaluate side-chains 110 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 109 optimal weight: 0.1980 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 0.0060 chunk 9 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4538 moved from start: 1.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9532 Z= 0.162 Angle : 0.645 9.229 12836 Z= 0.348 Chirality : 0.042 0.156 1388 Planarity : 0.004 0.040 1574 Dihedral : 4.497 16.844 1208 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.18 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.24), residues: 1100 helix: 0.56 (0.20), residues: 574 sheet: -0.17 (0.43), residues: 136 loop : -1.47 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 414 HIS 0.004 0.001 HIS A 201 PHE 0.046 0.002 PHE B 14 TYR 0.018 0.001 TYR B 441 ARG 0.005 0.001 ARG A 444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.7998 (t80) cc_final: 0.7620 (t80) REVERT: A 39 TRP cc_start: 0.7733 (m100) cc_final: 0.7231 (m-90) REVERT: A 110 TRP cc_start: 0.7413 (t60) cc_final: 0.7119 (t60) REVERT: A 122 LEU cc_start: 0.9219 (tp) cc_final: 0.8977 (tt) REVERT: A 126 LEU cc_start: 0.9036 (mt) cc_final: 0.8397 (mt) REVERT: A 130 TYR cc_start: 0.8434 (m-10) cc_final: 0.7934 (m-80) REVERT: A 138 LEU cc_start: 0.6128 (mt) cc_final: 0.5730 (mt) REVERT: A 178 TYR cc_start: 0.5551 (m-80) cc_final: 0.4875 (m-80) REVERT: A 198 ILE cc_start: 0.9241 (pt) cc_final: 0.8622 (pt) REVERT: A 199 ILE cc_start: 0.9558 (mm) cc_final: 0.9088 (mm) REVERT: A 208 ASN cc_start: 0.8873 (m-40) cc_final: 0.8231 (m110) REVERT: A 213 HIS cc_start: 0.7976 (m90) cc_final: 0.7770 (m170) REVERT: A 218 ASN cc_start: 0.8644 (t0) cc_final: 0.7867 (t0) REVERT: A 233 VAL cc_start: 0.8883 (m) cc_final: 0.8659 (m) REVERT: A 248 PHE cc_start: 0.6310 (m-10) cc_final: 0.5933 (m-10) REVERT: A 292 LYS cc_start: 0.7857 (tptt) cc_final: 0.7377 (ttpp) REVERT: A 295 LEU cc_start: 0.9213 (mt) cc_final: 0.8933 (mt) REVERT: A 302 ASN cc_start: 0.8156 (t0) cc_final: 0.7836 (t0) REVERT: A 317 PHE cc_start: 0.8798 (m-80) cc_final: 0.8438 (t80) REVERT: A 322 MET cc_start: 0.9197 (mpp) cc_final: 0.8832 (mpp) REVERT: A 365 MET cc_start: 0.1247 (tmm) cc_final: -0.0571 (tpp) REVERT: A 368 MET cc_start: -0.0130 (tpt) cc_final: -0.1318 (mtp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1512 time to fit residues: 24.1760 Evaluate side-chains 108 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.0070 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 4 optimal weight: 0.0060 chunk 63 optimal weight: 3.9990 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.188756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.144948 restraints weight = 13612.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.149181 restraints weight = 9357.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.152381 restraints weight = 6897.773| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 1.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9532 Z= 0.169 Angle : 0.628 8.278 12836 Z= 0.346 Chirality : 0.042 0.200 1388 Planarity : 0.004 0.044 1574 Dihedral : 4.395 19.234 1208 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.24), residues: 1100 helix: 0.56 (0.20), residues: 574 sheet: 0.02 (0.45), residues: 124 loop : -1.64 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 414 HIS 0.007 0.001 HIS A 418 PHE 0.048 0.002 PHE B 14 TYR 0.018 0.001 TYR B 441 ARG 0.005 0.001 ARG A 444 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1730.09 seconds wall clock time: 31 minutes 59.06 seconds (1919.06 seconds total)