Starting phenix.real_space_refine on Fri Dec 8 07:20:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sep_25074/12_2023/7sep_25074.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sep_25074/12_2023/7sep_25074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sep_25074/12_2023/7sep_25074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sep_25074/12_2023/7sep_25074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sep_25074/12_2023/7sep_25074.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sep_25074/12_2023/7sep_25074.pdb" } resolution = 3.8 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= 0.017 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 15 5.16 5 C 4967 2.51 5 N 1261 2.21 5 O 1398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7641 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4343 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 496} Chain breaks: 4 Chain: "B" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3298 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 368} Chain breaks: 3 Time building chain proxies: 4.25, per 1000 atoms: 0.56 Number of scatterers: 7641 At special positions: 0 Unit cell: (78.155, 98.455, 127.89, 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 15 16.00 O 1398 8.00 N 1261 7.00 C 4967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 40.4% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 3.928A pdb=" N ALA A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 124 through 127 Processing helix chain 'A' and resid 155 through 175 removed outlier: 3.731A pdb=" N ILE A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.907A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 271 removed outlier: 3.981A pdb=" N GLY A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 270 " --> pdb=" O TRP A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.520A pdb=" N THR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 311 Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 405 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.839A pdb=" N ILE A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 485 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.561A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.779A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 549 removed outlier: 3.515A pdb=" N GLN A 547 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.598A pdb=" N GLU B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.810A pdb=" N GLU B 89 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 90' Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.557A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 4.293A pdb=" N LYS B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 175 removed outlier: 4.052A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.504A pdb=" N TRP B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 removed outlier: 3.953A pdb=" N TRP B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 removed outlier: 4.219A pdb=" N LEU B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 311 Processing helix chain 'B' and resid 364 through 384 removed outlier: 3.540A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.679A pdb=" N THR B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.935A pdb=" N TRP B 406 " --> pdb=" O THR B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 422 through 428 removed outlier: 3.902A pdb=" N GLN B 428 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.843A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 338 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.592A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 391 removed outlier: 6.571A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 455 through 459 removed outlier: 4.136A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 494 " --> pdb=" O GLU A 438 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 49 removed outlier: 4.020A pdb=" N ILE B 142 " --> pdb=" O ILE B 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AB3, first strand: chain 'B' and resid 106 through 110 Processing sheet with id=AB4, first strand: chain 'B' and resid 347 through 355 removed outlier: 7.964A pdb=" N LYS B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN B 343 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR B 351 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR B 339 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS B 353 " --> pdb=" O TRP B 337 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP B 337 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 284 hydrogen bonds defined for protein. 768 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: 2.14 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1784 1.33 - 1.45: 1570 1.45 - 1.57: 4465 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 7845 Sorted by residual: bond pdb=" N ASP A 237 " pdb=" CA ASP A 237 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.10e-02 8.26e+03 9.83e+00 bond pdb=" N HIS A 235 " pdb=" CA HIS A 235 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.18e-02 7.18e+03 9.42e+00 bond pdb=" N LEU A 234 " pdb=" CA LEU A 234 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.30e-02 5.92e+03 6.92e+00 bond pdb=" N TRP A 239 " pdb=" CA TRP A 239 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.26e-02 6.30e+03 5.84e+00 bond pdb=" N THR A 240 " pdb=" CA THR A 240 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.54e+00 ... (remaining 7840 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.76: 317 106.76 - 113.71: 4428 113.71 - 120.66: 3198 120.66 - 127.62: 2587 127.62 - 134.57: 122 Bond angle restraints: 10652 Sorted by residual: angle pdb=" C HIS A 235 " pdb=" CA HIS A 235 " pdb=" CB HIS A 235 " ideal model delta sigma weight residual 108.87 115.04 -6.17 1.55e+00 4.16e-01 1.59e+01 angle pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" C PRO A 236 " ideal model delta sigma weight residual 112.47 119.69 -7.22 2.06e+00 2.36e-01 1.23e+01 angle pdb=" CA THR A 240 " pdb=" C THR A 240 " pdb=" O THR A 240 " ideal model delta sigma weight residual 121.45 117.82 3.63 1.07e+00 8.73e-01 1.15e+01 angle pdb=" CA LYS A 238 " pdb=" C LYS A 238 " pdb=" O LYS A 238 " ideal model delta sigma weight residual 121.51 118.20 3.31 1.12e+00 7.97e-01 8.71e+00 angle pdb=" C HIS A 235 " pdb=" N PRO A 236 " pdb=" CA PRO A 236 " ideal model delta sigma weight residual 119.84 123.26 -3.42 1.25e+00 6.40e-01 7.48e+00 ... (remaining 10647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 4317 16.64 - 33.27: 308 33.27 - 49.91: 78 49.91 - 66.54: 18 66.54 - 83.18: 4 Dihedral angle restraints: 4725 sinusoidal: 2009 harmonic: 2716 Sorted by residual: dihedral pdb=" CA LEU B 289 " pdb=" C LEU B 289 " pdb=" N THR B 290 " pdb=" CA THR B 290 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA PRO A 433 " pdb=" C PRO A 433 " pdb=" N ILE A 434 " pdb=" CA ILE A 434 " ideal model delta harmonic sigma weight residual -180.00 -159.97 -20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ASP B 185 " pdb=" C ASP B 185 " pdb=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 649 0.032 - 0.064: 326 0.064 - 0.096: 119 0.096 - 0.128: 54 0.128 - 0.160: 9 Chirality restraints: 1157 Sorted by residual: chirality pdb=" CB ILE A 434 " pdb=" CA ILE A 434 " pdb=" CG1 ILE A 434 " pdb=" CG2 ILE A 434 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA PRO A 236 " pdb=" N PRO A 236 " pdb=" C PRO A 236 " pdb=" CB PRO A 236 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA PRO B 140 " pdb=" N PRO B 140 " pdb=" C PRO B 140 " pdb=" CB PRO B 140 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 1154 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 420 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 421 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 239 " 0.024 2.00e-02 2.50e+03 1.25e-02 3.88e+00 pdb=" CG TRP A 239 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 239 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 239 " -0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP A 239 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 239 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 239 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 239 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 239 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 239 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 411 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO B 412 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 412 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 412 " 0.025 5.00e-02 4.00e+02 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 270 2.70 - 3.25: 7642 3.25 - 3.80: 11915 3.80 - 4.35: 13907 4.35 - 4.90: 23690 Nonbonded interactions: 57424 Sorted by model distance: nonbonded pdb=" N ASN A 545 " pdb=" OD1 ASN A 545 " model vdw 2.155 2.520 nonbonded pdb=" O SER A 162 " pdb=" OG1 THR A 165 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR B 354 " pdb=" OE1 GLU B 370 " model vdw 2.228 2.440 nonbonded pdb=" OG1 THR A 419 " pdb=" O PRO A 421 " model vdw 2.234 2.440 nonbonded pdb=" OG1 THR B 253 " pdb=" O GLU B 291 " model vdw 2.240 2.440 ... (remaining 57419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.800 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 22.590 Find NCS groups from input model: 0.190 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 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 : 0.006 0.048 7845 Z= 0.383 Angle : 0.659 8.506 10652 Z= 0.378 Chirality : 0.046 0.160 1157 Planarity : 0.006 0.050 1335 Dihedral : 12.759 83.180 2969 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 8.22 % Allowed : 8.94 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.19 (0.29), residues: 912 helix: 1.24 (0.31), residues: 297 sheet: -0.86 (0.42), residues: 150 loop : -0.73 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 239 HIS 0.006 0.001 HIS A 235 PHE 0.011 0.002 PHE A 124 TYR 0.019 0.002 TYR A 441 ARG 0.004 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 386 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 28 residues processed: 426 average time/residue: 0.2245 time to fit residues: 123.3493 Evaluate side-chains 362 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 334 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.0832 time to fit residues: 5.3508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 0.0070 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 367 GLN A 373 GLN A 480 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7845 Z= 0.253 Angle : 0.647 9.538 10652 Z= 0.339 Chirality : 0.046 0.250 1157 Planarity : 0.006 0.088 1335 Dihedral : 4.842 18.303 986 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.65 % Allowed : 23.00 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.23 (0.28), residues: 912 helix: 1.05 (0.30), residues: 318 sheet: -0.65 (0.41), residues: 140 loop : -0.83 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 337 HIS 0.004 0.001 HIS B 198 PHE 0.030 0.002 PHE A 124 TYR 0.027 0.002 TYR A 319 ARG 0.005 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 328 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 20 residues processed: 346 average time/residue: 0.2181 time to fit residues: 97.3741 Evaluate side-chains 328 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 308 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0772 time to fit residues: 3.9796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 69 optimal weight: 0.0770 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 348 ASN A 367 GLN A 480 GLN A 507 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 96 HIS ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN B 394 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7845 Z= 0.200 Angle : 0.628 8.809 10652 Z= 0.323 Chirality : 0.045 0.255 1157 Planarity : 0.005 0.052 1335 Dihedral : 4.557 15.861 986 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.69 % Allowed : 26.46 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.32 (0.28), residues: 912 helix: 1.01 (0.30), residues: 317 sheet: -0.62 (0.41), residues: 140 loop : -0.92 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 266 HIS 0.007 0.001 HIS A 208 PHE 0.020 0.002 PHE A 124 TYR 0.027 0.002 TYR A 483 ARG 0.003 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 313 time to evaluate : 0.856 Fit side-chains outliers start: 31 outliers final: 16 residues processed: 322 average time/residue: 0.2264 time to fit residues: 94.8189 Evaluate side-chains 331 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 315 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1175 time to fit residues: 4.1796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 43 optimal weight: 0.0040 chunk 9 optimal weight: 0.0770 chunk 39 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 85 GLN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7845 Z= 0.175 Angle : 0.598 9.026 10652 Z= 0.307 Chirality : 0.044 0.152 1157 Planarity : 0.005 0.050 1335 Dihedral : 4.378 14.445 986 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.86 % Allowed : 26.94 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.28), residues: 912 helix: 0.92 (0.30), residues: 318 sheet: -0.57 (0.41), residues: 140 loop : -0.90 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 266 HIS 0.005 0.001 HIS A 208 PHE 0.019 0.002 PHE A 171 TYR 0.025 0.002 TYR A 181 ARG 0.002 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 323 time to evaluate : 0.880 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 330 average time/residue: 0.2169 time to fit residues: 92.9140 Evaluate side-chains 331 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 314 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0826 time to fit residues: 3.7526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 81 ASN B 373 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 7845 Z= 0.417 Angle : 0.729 8.494 10652 Z= 0.390 Chirality : 0.050 0.187 1157 Planarity : 0.006 0.055 1335 Dihedral : 5.337 22.847 986 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.81 % Allowed : 28.37 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.99 (0.28), residues: 912 helix: 0.42 (0.29), residues: 312 sheet: -1.16 (0.39), residues: 145 loop : -1.21 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 337 HIS 0.004 0.001 HIS B 198 PHE 0.024 0.002 PHE A 171 TYR 0.033 0.003 TYR A 181 ARG 0.005 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 325 time to evaluate : 0.932 Fit side-chains outliers start: 32 outliers final: 20 residues processed: 332 average time/residue: 0.2161 time to fit residues: 93.5261 Evaluate side-chains 330 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 310 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1005 time to fit residues: 4.6110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 0.0030 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 81 ASN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7845 Z= 0.204 Angle : 0.640 10.164 10652 Z= 0.328 Chirality : 0.045 0.225 1157 Planarity : 0.005 0.049 1335 Dihedral : 4.732 17.677 986 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.38 % Allowed : 29.68 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.28), residues: 912 helix: 0.74 (0.31), residues: 311 sheet: -0.94 (0.40), residues: 140 loop : -0.98 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 401 HIS 0.005 0.001 HIS A 208 PHE 0.024 0.002 PHE A 171 TYR 0.026 0.002 TYR A 319 ARG 0.003 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 305 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 313 average time/residue: 0.2282 time to fit residues: 92.5722 Evaluate side-chains 316 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 305 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0874 time to fit residues: 2.9114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 0.0170 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 81 ASN B 332 GLN B 373 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7845 Z= 0.196 Angle : 0.642 10.737 10652 Z= 0.326 Chirality : 0.046 0.234 1157 Planarity : 0.005 0.047 1335 Dihedral : 4.568 18.121 986 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.74 % Allowed : 29.68 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.55 (0.28), residues: 912 helix: 0.71 (0.30), residues: 311 sheet: -0.85 (0.40), residues: 140 loop : -0.91 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 337 HIS 0.005 0.001 HIS A 208 PHE 0.021 0.002 PHE A 171 TYR 0.029 0.002 TYR A 319 ARG 0.003 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 308 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 314 average time/residue: 0.2312 time to fit residues: 93.8903 Evaluate side-chains 311 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 297 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1417 time to fit residues: 4.1409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 81 ASN B 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7845 Z= 0.227 Angle : 0.671 10.987 10652 Z= 0.338 Chirality : 0.045 0.192 1157 Planarity : 0.005 0.043 1335 Dihedral : 4.611 18.016 986 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.19 % Allowed : 30.87 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.53 (0.28), residues: 912 helix: 0.70 (0.30), residues: 311 sheet: -0.79 (0.41), residues: 140 loop : -0.89 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 337 HIS 0.008 0.001 HIS A 235 PHE 0.019 0.002 PHE A 171 TYR 0.029 0.002 TYR A 319 ARG 0.002 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 301 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 304 average time/residue: 0.2185 time to fit residues: 86.0083 Evaluate side-chains 305 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 298 time to evaluate : 0.667 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0650 time to fit residues: 1.7783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 81 ASN B 332 GLN B 373 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7845 Z= 0.234 Angle : 0.700 11.140 10652 Z= 0.353 Chirality : 0.046 0.199 1157 Planarity : 0.006 0.093 1335 Dihedral : 4.741 19.908 986 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.55 % Allowed : 32.54 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.48 (0.28), residues: 912 helix: 0.82 (0.31), residues: 303 sheet: -0.81 (0.40), residues: 152 loop : -0.87 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 337 HIS 0.005 0.001 HIS A 208 PHE 0.039 0.002 PHE A 87 TYR 0.032 0.002 TYR A 319 ARG 0.017 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 296 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 298 average time/residue: 0.2011 time to fit residues: 78.0498 Evaluate side-chains 299 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 291 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0871 time to fit residues: 2.3113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 81 ASN B 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7845 Z= 0.254 Angle : 0.715 11.182 10652 Z= 0.363 Chirality : 0.047 0.202 1157 Planarity : 0.005 0.044 1335 Dihedral : 4.727 19.821 986 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.72 % Allowed : 33.73 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.28), residues: 912 helix: 0.77 (0.30), residues: 303 sheet: -0.82 (0.40), residues: 152 loop : -0.80 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 398 HIS 0.005 0.001 HIS A 208 PHE 0.031 0.003 PHE A 87 TYR 0.030 0.002 TYR A 319 ARG 0.002 0.000 ARG B 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 294 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 294 average time/residue: 0.2339 time to fit residues: 88.8182 Evaluate side-chains 296 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 293 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0792 time to fit residues: 1.7004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 0.0170 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 475 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 81 ASN B 332 GLN B 373 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.132047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114869 restraints weight = 14049.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118721 restraints weight = 7050.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121266 restraints weight = 4269.943| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7845 Z= 0.230 Angle : 0.711 11.159 10652 Z= 0.358 Chirality : 0.047 0.198 1157 Planarity : 0.005 0.042 1335 Dihedral : 4.664 19.290 986 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.83 % Allowed : 35.16 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.28), residues: 912 helix: 0.77 (0.31), residues: 303 sheet: -0.78 (0.39), residues: 150 loop : -0.79 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 398 HIS 0.009 0.001 HIS A 208 PHE 0.029 0.003 PHE A 87 TYR 0.035 0.002 TYR A 501 ARG 0.001 0.000 ARG B 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2348.08 seconds wall clock time: 45 minutes 57.80 seconds (2757.80 seconds total)