Starting phenix.real_space_refine on Fri Aug 2 22:11:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u0j_41781/08_2024/8u0j_41781.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u0j_41781/08_2024/8u0j_41781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u0j_41781/08_2024/8u0j_41781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u0j_41781/08_2024/8u0j_41781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u0j_41781/08_2024/8u0j_41781.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u0j_41781/08_2024/8u0j_41781.cif" } resolution = 3.1 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= -0.000 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 1 5.21 5 S 10 5.16 5 C 3466 2.51 5 N 963 2.21 5 O 1169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 19": "OE1" <-> "OE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 486": "NH1" <-> "NH2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 541": "OE1" <-> "OE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 568": "OE1" <-> "OE2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 684": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 5657 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4669 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 540} Chain breaks: 1 Chain: "B" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "F" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 226 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.25, per 1000 atoms: 0.75 Number of scatterers: 5657 At special positions: 0 Unit cell: (83.32, 81.6536, 102.484, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 P 48 15.00 Mg 1 11.99 O 1169 8.00 N 963 7.00 C 3466 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: 2.54 Conformation dependent library (CDL) restraints added in 1.0 seconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1074 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 6 sheets defined 36.7% alpha, 13.2% beta 9 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 249 through 266 Processing helix chain 'A' and resid 285 through 301 Processing helix chain 'A' and resid 317 through 328 removed outlier: 3.618A pdb=" N THR A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.701A pdb=" N TYR A 355 " --> pdb=" O LYS A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.834A pdb=" N VAL A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG A 367 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.529A pdb=" N TRP A 384 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 410 removed outlier: 4.174A pdb=" N VAL A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 4.015A pdb=" N ARG A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.729A pdb=" N LEU A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 4.310A pdb=" N ARG A 478 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS A 479 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 528 removed outlier: 3.772A pdb=" N GLU A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 542 Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.535A pdb=" N GLU A 568 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR A 571 " --> pdb=" O GLU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 589 Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.909A pdb=" N LEU A 655 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A 656 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 657 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.808A pdb=" N LYS A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A 675 " --> pdb=" O TYR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 684 No H-bonds generated for 'chain 'A' and resid 682 through 684' Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 144 removed outlier: 5.757A pdb=" N TYR A 137 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE A 159 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU A 139 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 157 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 336 removed outlier: 7.052A pdb=" N LEU A 305 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ALA A 336 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE A 307 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASN A 345 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N CYS A 378 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU A 347 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 455 through 460 removed outlier: 7.228A pdb=" N LEU A 638 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 506 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER A 636 " --> pdb=" O ILE A 506 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 612 through 613 removed outlier: 3.917A pdb=" N PHE A 621 " --> pdb=" O PHE A 612 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 940 1.32 - 1.44: 1776 1.44 - 1.57: 3064 1.57 - 1.69: 93 1.69 - 1.81: 16 Bond restraints: 5889 Sorted by residual: bond pdb=" CB VAL A 680 " pdb=" CG1 VAL A 680 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.67e+00 bond pdb=" C GLU A 416 " pdb=" N TYR A 417 " ideal model delta sigma weight residual 1.329 1.293 0.036 1.86e-02 2.89e+03 3.78e+00 bond pdb=" N SER A 436 " pdb=" CA SER A 436 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.19e+00 bond pdb=" CG PHE A 656 " pdb=" CD1 PHE A 656 " ideal model delta sigma weight residual 1.384 1.348 0.036 2.10e-02 2.27e+03 2.96e+00 bond pdb=" CB VAL A 251 " pdb=" CG1 VAL A 251 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.77e+00 ... (remaining 5884 not shown) Histogram of bond angle deviations from ideal: 93.55 - 101.64: 37 101.64 - 109.73: 1295 109.73 - 117.82: 3208 117.82 - 125.91: 3382 125.91 - 134.00: 247 Bond angle restraints: 8169 Sorted by residual: angle pdb=" C TYR A 363 " pdb=" N GLN A 364 " pdb=" CA GLN A 364 " ideal model delta sigma weight residual 121.54 131.52 -9.98 1.91e+00 2.74e-01 2.73e+01 angle pdb=" C PRO A 563 " pdb=" N LEU A 564 " pdb=" CA LEU A 564 " ideal model delta sigma weight residual 121.61 127.34 -5.73 1.39e+00 5.18e-01 1.70e+01 angle pdb=" C CYS A 378 " pdb=" N TYR A 379 " pdb=" CA TYR A 379 " ideal model delta sigma weight residual 121.48 129.48 -8.00 2.04e+00 2.40e-01 1.54e+01 angle pdb=" N SER A 608 " pdb=" CA SER A 608 " pdb=" C SER A 608 " ideal model delta sigma weight residual 114.09 108.35 5.74 1.55e+00 4.16e-01 1.37e+01 angle pdb=" C GLN A 430 " pdb=" N ARG A 431 " pdb=" CA ARG A 431 " ideal model delta sigma weight residual 120.94 127.94 -7.00 1.90e+00 2.77e-01 1.36e+01 ... (remaining 8164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2770 17.94 - 35.88: 404 35.88 - 53.82: 189 53.82 - 71.76: 47 71.76 - 89.70: 9 Dihedral angle restraints: 3419 sinusoidal: 1749 harmonic: 1670 Sorted by residual: dihedral pdb=" CA SER A 437 " pdb=" C SER A 437 " pdb=" N GLU A 438 " pdb=" CA GLU A 438 " ideal model delta harmonic sigma weight residual -180.00 -125.52 -54.48 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA GLU A 435 " pdb=" C GLU A 435 " pdb=" N SER A 436 " pdb=" CA SER A 436 " ideal model delta harmonic sigma weight residual -180.00 -140.41 -39.59 0 5.00e+00 4.00e-02 6.27e+01 dihedral pdb=" CA TYR A 220 " pdb=" C TYR A 220 " pdb=" N ILE A 221 " pdb=" CA ILE A 221 " ideal model delta harmonic sigma weight residual 180.00 -158.53 -21.47 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 3416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 648 0.051 - 0.102: 186 0.102 - 0.153: 35 0.153 - 0.204: 8 0.204 - 0.255: 1 Chirality restraints: 878 Sorted by residual: chirality pdb=" CA PHE A 656 " pdb=" N PHE A 656 " pdb=" C PHE A 656 " pdb=" CB PHE A 656 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA GLN A 364 " pdb=" N GLN A 364 " pdb=" C GLN A 364 " pdb=" CB GLN A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB VAL A 480 " pdb=" CA VAL A 480 " pdb=" CG1 VAL A 480 " pdb=" CG2 VAL A 480 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 875 not shown) Planarity restraints: 889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 364 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C GLN A 364 " 0.058 2.00e-02 2.50e+03 pdb=" O GLN A 364 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 365 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 428 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO A 429 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 429 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 429 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 363 " 0.015 2.00e-02 2.50e+03 1.39e-02 3.84e+00 pdb=" CG TYR A 363 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 363 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 363 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 363 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 363 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 363 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 363 " -0.000 2.00e-02 2.50e+03 ... (remaining 886 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 313 2.72 - 3.26: 5253 3.26 - 3.81: 9454 3.81 - 4.35: 11941 4.35 - 4.90: 19173 Nonbonded interactions: 46134 Sorted by model distance: nonbonded pdb=" OP1 DT B 3 " pdb="MG MG B 101 " model vdw 2.170 2.170 nonbonded pdb=" OH TYR A 620 " pdb=" O VAL A 668 " model vdw 2.204 3.040 nonbonded pdb=" OG SER A 576 " pdb=" OP1 DA D 23 " model vdw 2.250 3.040 nonbonded pdb=" NH1 ARG A 202 " pdb=" O GLY A 218 " model vdw 2.256 3.120 nonbonded pdb=" O2 DT D 20 " pdb=" N2 DG F 9 " model vdw 2.300 3.120 ... (remaining 46129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 22.700 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 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 : 0.008 0.103 5889 Z= 0.472 Angle : 0.915 9.980 8169 Z= 0.526 Chirality : 0.050 0.255 878 Planarity : 0.006 0.057 889 Dihedral : 20.282 89.698 2345 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % 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 : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.34), residues: 565 helix: 0.11 (0.40), residues: 154 sheet: -0.19 (0.53), residues: 90 loop : -1.30 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 444 HIS 0.006 0.002 HIS A 660 PHE 0.025 0.003 PHE A 685 TYR 0.034 0.003 TYR A 363 ARG 0.017 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.579 Fit side-chains REVERT: A 302 GLU cc_start: 0.7306 (tp30) cc_final: 0.6769 (tm-30) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2135 time to fit residues: 22.8302 Evaluate side-chains 72 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5889 Z= 0.262 Angle : 0.644 7.507 8169 Z= 0.355 Chirality : 0.042 0.153 878 Planarity : 0.006 0.044 889 Dihedral : 23.030 74.002 1166 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.98 % Allowed : 8.43 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.35), residues: 565 helix: 0.75 (0.41), residues: 157 sheet: -0.07 (0.53), residues: 91 loop : -1.25 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 585 HIS 0.004 0.001 HIS A 281 PHE 0.025 0.002 PHE A 611 TYR 0.015 0.002 TYR A 293 ARG 0.004 0.000 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.581 Fit side-chains REVERT: A 19 GLU cc_start: 0.5723 (tp30) cc_final: 0.5484 (tp30) REVERT: A 302 GLU cc_start: 0.7341 (tp30) cc_final: 0.6882 (tm-30) REVERT: A 440 ARG cc_start: 0.6637 (mmm160) cc_final: 0.5857 (mmm160) outliers start: 5 outliers final: 3 residues processed: 84 average time/residue: 0.2070 time to fit residues: 22.1688 Evaluate side-chains 80 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 597 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5889 Z= 0.244 Angle : 0.606 6.911 8169 Z= 0.333 Chirality : 0.041 0.153 878 Planarity : 0.005 0.042 889 Dihedral : 22.947 74.760 1166 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.18 % Allowed : 12.16 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.44 (0.36), residues: 565 helix: 1.13 (0.41), residues: 157 sheet: 0.05 (0.53), residues: 92 loop : -1.16 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 456 HIS 0.004 0.001 HIS A 281 PHE 0.013 0.002 PHE A 484 TYR 0.013 0.002 TYR A 671 ARG 0.002 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7353 (tp30) cc_final: 0.6972 (tm-30) REVERT: A 341 ARG cc_start: 0.7057 (mtm110) cc_final: 0.6556 (mtp180) REVERT: A 440 ARG cc_start: 0.6615 (mmm160) cc_final: 0.5885 (mmm160) REVERT: A 619 MET cc_start: 0.5649 (mtm) cc_final: 0.5316 (mtm) outliers start: 6 outliers final: 4 residues processed: 83 average time/residue: 0.2115 time to fit residues: 22.2570 Evaluate side-chains 78 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 632 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN A 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 5889 Z= 0.331 Angle : 0.646 6.397 8169 Z= 0.351 Chirality : 0.042 0.158 878 Planarity : 0.005 0.044 889 Dihedral : 23.083 76.620 1166 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.35 % Allowed : 13.14 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.52 (0.36), residues: 565 helix: 1.10 (0.41), residues: 156 sheet: -0.08 (0.52), residues: 92 loop : -1.20 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 456 HIS 0.005 0.001 HIS A 281 PHE 0.028 0.002 PHE A 611 TYR 0.015 0.002 TYR A 671 ARG 0.003 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7339 (tp30) cc_final: 0.7001 (tm-30) REVERT: A 341 ARG cc_start: 0.7049 (mtm110) cc_final: 0.6539 (mtp180) REVERT: A 440 ARG cc_start: 0.6652 (mmm160) cc_final: 0.5870 (mmm160) REVERT: A 611 PHE cc_start: 0.7217 (t80) cc_final: 0.6921 (t80) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 0.2103 time to fit residues: 23.0946 Evaluate side-chains 82 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5889 Z= 0.234 Angle : 0.588 6.244 8169 Z= 0.323 Chirality : 0.040 0.152 878 Planarity : 0.005 0.044 889 Dihedral : 22.868 69.698 1166 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.57 % Allowed : 14.51 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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 (0.36), residues: 565 helix: 1.36 (0.41), residues: 157 sheet: -0.03 (0.52), residues: 92 loop : -1.13 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 456 HIS 0.002 0.001 HIS A 281 PHE 0.023 0.002 PHE A 611 TYR 0.012 0.001 TYR A 671 ARG 0.002 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7299 (tp30) cc_final: 0.6987 (tm-30) REVERT: A 341 ARG cc_start: 0.7048 (mtm110) cc_final: 0.6530 (mtp180) REVERT: A 440 ARG cc_start: 0.6515 (mmm160) cc_final: 0.5669 (mmm160) REVERT: A 509 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7857 (mt) REVERT: A 578 ASP cc_start: 0.7921 (t0) cc_final: 0.7700 (t0) REVERT: A 611 PHE cc_start: 0.7106 (t80) cc_final: 0.6903 (t80) REVERT: A 619 MET cc_start: 0.5563 (mtm) cc_final: 0.5284 (mtm) outliers start: 8 outliers final: 6 residues processed: 82 average time/residue: 0.2049 time to fit residues: 21.5706 Evaluate side-chains 79 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.0060 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5889 Z= 0.239 Angle : 0.583 5.975 8169 Z= 0.319 Chirality : 0.040 0.152 878 Planarity : 0.005 0.044 889 Dihedral : 22.882 72.875 1166 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.76 % Allowed : 15.49 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.29 (0.36), residues: 565 helix: 1.48 (0.42), residues: 156 sheet: -0.11 (0.52), residues: 92 loop : -1.11 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 456 HIS 0.002 0.001 HIS A 643 PHE 0.019 0.002 PHE A 611 TYR 0.012 0.001 TYR A 671 ARG 0.002 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7308 (tp30) cc_final: 0.6984 (tm-30) REVERT: A 341 ARG cc_start: 0.7036 (mtm110) cc_final: 0.6521 (mtp180) REVERT: A 417 TYR cc_start: 0.7617 (m-80) cc_final: 0.7303 (m-80) REVERT: A 440 ARG cc_start: 0.6555 (mmm160) cc_final: 0.5580 (mmm160) REVERT: A 509 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7881 (mt) outliers start: 9 outliers final: 8 residues processed: 80 average time/residue: 0.2225 time to fit residues: 22.5400 Evaluate side-chains 78 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.0000 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5889 Z= 0.213 Angle : 0.573 6.094 8169 Z= 0.315 Chirality : 0.040 0.150 878 Planarity : 0.005 0.043 889 Dihedral : 22.840 70.522 1166 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.37 % Allowed : 16.86 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.17 (0.36), residues: 565 helix: 1.64 (0.42), residues: 156 sheet: -0.12 (0.52), residues: 92 loop : -1.04 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 456 HIS 0.003 0.001 HIS A 281 PHE 0.015 0.002 PHE A 685 TYR 0.012 0.001 TYR A 620 ARG 0.001 0.000 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7313 (tp30) cc_final: 0.6979 (tm-30) REVERT: A 341 ARG cc_start: 0.7027 (mtm110) cc_final: 0.6486 (mtp180) REVERT: A 417 TYR cc_start: 0.7597 (m-80) cc_final: 0.7254 (m-80) REVERT: A 440 ARG cc_start: 0.6516 (mmm160) cc_final: 0.5460 (mmm160) REVERT: A 509 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7823 (mt) REVERT: A 619 MET cc_start: 0.5351 (mtm) cc_final: 0.5058 (mtp) outliers start: 7 outliers final: 6 residues processed: 80 average time/residue: 0.2065 time to fit residues: 20.9868 Evaluate side-chains 78 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.0570 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5889 Z= 0.226 Angle : 0.583 6.519 8169 Z= 0.317 Chirality : 0.040 0.150 878 Planarity : 0.005 0.044 889 Dihedral : 22.880 71.627 1166 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.96 % Allowed : 16.67 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.17 (0.36), residues: 565 helix: 1.64 (0.41), residues: 156 sheet: -0.09 (0.52), residues: 92 loop : -1.05 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 456 HIS 0.002 0.001 HIS A 643 PHE 0.023 0.002 PHE A 621 TYR 0.012 0.001 TYR A 671 ARG 0.001 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7401 (tp30) cc_final: 0.6951 (tm-30) REVERT: A 341 ARG cc_start: 0.7017 (mtm110) cc_final: 0.6479 (mtp180) REVERT: A 417 TYR cc_start: 0.7584 (m-80) cc_final: 0.7214 (m-80) REVERT: A 440 ARG cc_start: 0.6495 (mmm160) cc_final: 0.5347 (mmm160) REVERT: A 509 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7807 (mt) REVERT: A 619 MET cc_start: 0.5407 (mtm) cc_final: 0.5112 (mtp) outliers start: 10 outliers final: 8 residues processed: 75 average time/residue: 0.2187 time to fit residues: 20.9174 Evaluate side-chains 78 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.0050 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5889 Z= 0.214 Angle : 0.579 6.617 8169 Z= 0.315 Chirality : 0.039 0.150 878 Planarity : 0.005 0.043 889 Dihedral : 22.887 71.108 1166 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.76 % Allowed : 17.06 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.10 (0.36), residues: 565 helix: 1.70 (0.41), residues: 156 sheet: -0.01 (0.52), residues: 92 loop : -1.02 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 456 HIS 0.002 0.001 HIS A 643 PHE 0.023 0.002 PHE A 621 TYR 0.012 0.001 TYR A 671 ARG 0.001 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7354 (tp30) cc_final: 0.6871 (tm-30) REVERT: A 341 ARG cc_start: 0.7014 (mtm110) cc_final: 0.6480 (mtp180) REVERT: A 417 TYR cc_start: 0.7536 (m-80) cc_final: 0.7160 (m-80) REVERT: A 435 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6787 (pm20) REVERT: A 440 ARG cc_start: 0.6469 (mmm160) cc_final: 0.5276 (mmm160) REVERT: A 482 HIS cc_start: 0.6864 (t-90) cc_final: 0.6277 (t-90) REVERT: A 509 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7819 (mt) REVERT: A 619 MET cc_start: 0.5344 (mtm) cc_final: 0.5081 (mtp) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.2087 time to fit residues: 20.8590 Evaluate side-chains 78 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5889 Z= 0.261 Angle : 0.600 6.195 8169 Z= 0.327 Chirality : 0.040 0.151 878 Planarity : 0.005 0.044 889 Dihedral : 22.931 75.132 1166 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.96 % Allowed : 16.86 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.36), residues: 565 helix: 1.55 (0.41), residues: 156 sheet: -0.01 (0.52), residues: 92 loop : -1.05 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 185 HIS 0.002 0.001 HIS A 643 PHE 0.024 0.002 PHE A 621 TYR 0.013 0.002 TYR A 671 ARG 0.002 0.000 ARG A 367 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.593 Fit side-chains REVERT: A 302 GLU cc_start: 0.7345 (tp30) cc_final: 0.6854 (tm-30) REVERT: A 341 ARG cc_start: 0.7024 (mtm110) cc_final: 0.6491 (mtp85) REVERT: A 364 GLN cc_start: 0.6140 (OUTLIER) cc_final: 0.5885 (pt0) REVERT: A 417 TYR cc_start: 0.7617 (m-80) cc_final: 0.7227 (m-80) REVERT: A 440 ARG cc_start: 0.6394 (mmm160) cc_final: 0.5029 (mmm160) outliers start: 10 outliers final: 9 residues processed: 76 average time/residue: 0.2306 time to fit residues: 22.5689 Evaluate side-chains 76 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.0570 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.0370 chunk 38 optimal weight: 0.6980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.234511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.187699 restraints weight = 6408.359| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 3.23 r_work: 0.3998 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5889 Z= 0.192 Angle : 0.567 5.960 8169 Z= 0.310 Chirality : 0.039 0.150 878 Planarity : 0.005 0.045 889 Dihedral : 22.825 70.564 1166 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.37 % Allowed : 17.65 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.02 (0.36), residues: 565 helix: 1.80 (0.42), residues: 156 sheet: 0.09 (0.52), residues: 92 loop : -0.95 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 444 HIS 0.002 0.001 HIS A 643 PHE 0.021 0.002 PHE A 621 TYR 0.011 0.001 TYR A 491 ARG 0.002 0.000 ARG A 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1604.02 seconds wall clock time: 29 minutes 3.26 seconds (1743.26 seconds total)