Starting phenix.real_space_refine on Sun Mar 10 18:58:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/03_2024/8k6l_36922_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/03_2024/8k6l_36922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/03_2024/8k6l_36922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/03_2024/8k6l_36922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/03_2024/8k6l_36922_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/03_2024/8k6l_36922_updated.pdb" } resolution = 2.92 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= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 34 5.16 5 Cl 2 4.86 5 C 2749 2.51 5 N 651 2.21 5 O 719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A ARG 58": "NH1" <-> "NH2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 527": "OD1" <-> "OD2" Residue "A ASP 528": "OD1" <-> "OD2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 596": "OD1" <-> "OD2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4155 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4086 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 18, 'TRANS': 528} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'ASP:plan': 4, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'IOQ': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.28, per 1000 atoms: 0.79 Number of scatterers: 4155 At special positions: 0 Unit cell: (65.24, 100.656, 87.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 34 16.00 O 719 8.00 N 651 7.00 C 2749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.04 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=1.71 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 802 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 698.9 milliseconds 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 996 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 0 sheets defined 61.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 27 through 50 removed outlier: 3.725A pdb=" N ALA A 33 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.800A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.676A pdb=" N SER A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 117 removed outlier: 3.808A pdb=" N THR A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 171 through 198 removed outlier: 4.252A pdb=" N THR A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Proline residue: A 187 - end of helix Proline residue: A 190 - end of helix removed outlier: 3.741A pdb=" N SER A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 232 removed outlier: 4.429A pdb=" N MET A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLY A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Proline residue: A 220 - end of helix removed outlier: 3.865A pdb=" N SER A 228 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.922A pdb=" N VAL A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.810A pdb=" N ILE A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 366 removed outlier: 5.301A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 400 removed outlier: 3.865A pdb=" N VAL A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Proline residue: A 384 - end of helix removed outlier: 3.514A pdb=" N ILE A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 427 removed outlier: 3.876A pdb=" N PHE A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 528 through 549 removed outlier: 3.542A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 587 through 598 removed outlier: 4.276A pdb=" N THR A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N THR A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 650 210 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 1.72 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: 881 1.33 - 1.45: 1009 1.45 - 1.57: 2315 1.57 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 4258 Sorted by residual: bond pdb=" C THR A 186 " pdb=" N PRO A 187 " ideal model delta sigma weight residual 1.331 1.371 -0.039 7.90e-03 1.60e+04 2.44e+01 bond pdb=" C SER A 140 " pdb=" N THR A 141 " ideal model delta sigma weight residual 1.332 1.291 0.041 1.40e-02 5.10e+03 8.70e+00 bond pdb=" C PHE A 591 " pdb=" O PHE A 591 " ideal model delta sigma weight residual 1.237 1.210 0.026 1.17e-02 7.31e+03 5.05e+00 bond pdb=" C PRO A 588 " pdb=" O PRO A 588 " ideal model delta sigma weight residual 1.237 1.211 0.026 1.16e-02 7.43e+03 4.98e+00 bond pdb=" C ILE A 589 " pdb=" O ILE A 589 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.13e-02 7.83e+03 4.97e+00 ... (remaining 4253 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.02: 112 107.02 - 113.77: 2343 113.77 - 120.51: 1776 120.51 - 127.26: 1513 127.26 - 134.01: 38 Bond angle restraints: 5782 Sorted by residual: angle pdb=" C ILE A 585 " pdb=" CA ILE A 585 " pdb=" CB ILE A 585 " ideal model delta sigma weight residual 111.30 101.87 9.43 9.60e-01 1.09e+00 9.65e+01 angle pdb=" N ILE A 52 " pdb=" CA ILE A 52 " pdb=" C ILE A 52 " ideal model delta sigma weight residual 110.62 117.58 -6.96 1.02e+00 9.61e-01 4.65e+01 angle pdb=" N ASN A 375 " pdb=" CA ASN A 375 " pdb=" C ASN A 375 " ideal model delta sigma weight residual 111.02 120.98 -9.96 1.52e+00 4.33e-01 4.30e+01 angle pdb=" C ALA A 32 " pdb=" N ALA A 33 " pdb=" CA ALA A 33 " ideal model delta sigma weight residual 120.28 129.02 -8.74 1.34e+00 5.57e-01 4.25e+01 angle pdb=" C THR A 186 " pdb=" N PRO A 187 " pdb=" CA PRO A 187 " ideal model delta sigma weight residual 121.00 113.85 7.15 1.16e+00 7.43e-01 3.80e+01 ... (remaining 5777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.07: 2317 21.07 - 42.14: 131 42.14 - 63.21: 43 63.21 - 84.28: 4 84.28 - 105.35: 16 Dihedral angle restraints: 2511 sinusoidal: 947 harmonic: 1564 Sorted by residual: dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -157.45 71.45 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS A 599 " pdb=" SG CYS A 599 " pdb=" SG CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sinusoidal sigma weight residual -86.00 -155.91 69.91 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" C TYR A 590 " pdb=" N TYR A 590 " pdb=" CA TYR A 590 " pdb=" CB TYR A 590 " ideal model delta harmonic sigma weight residual -122.60 -139.33 16.73 0 2.50e+00 1.60e-01 4.48e+01 ... (remaining 2508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 672 0.243 - 0.486: 2 0.486 - 0.729: 2 0.729 - 0.972: 1 0.972 - 1.215: 1 Chirality restraints: 678 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.13e+02 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 503 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.69e+01 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 516 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.16e+01 ... (remaining 675 not shown) Planarity restraints: 702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.339 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG B 1 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.094 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.310 2.00e-02 2.50e+03 2.61e-01 8.49e+02 pdb=" C7 NAG B 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.448 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " 0.309 2.00e-02 2.50e+03 2.60e-01 8.48e+02 pdb=" C7 NAG A 802 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " -0.448 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " 0.030 2.00e-02 2.50e+03 ... (remaining 699 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1281 2.82 - 3.34: 3843 3.34 - 3.86: 6430 3.86 - 4.38: 7227 4.38 - 4.90: 12370 Nonbonded interactions: 31151 Sorted by model distance: nonbonded pdb=" O SER A 85 " pdb=" OG SER A 89 " model vdw 2.297 2.440 nonbonded pdb=" O GLY A 324 " pdb=" OG SER A 328 " model vdw 2.387 2.440 nonbonded pdb=" O LEU A 507 " pdb=" CD1 LEU A 507 " model vdw 2.400 3.460 nonbonded pdb=" O SER A 491 " pdb=" CD1 PHE A 501 " model vdw 2.463 3.340 nonbonded pdb=" O SER A 371 " pdb=" OG SER A 371 " model vdw 2.475 2.440 ... (remaining 31146 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 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: 0.770 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: 3.740 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 16.070 Find NCS groups from input model: 0.290 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:14.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.005 0.041 4258 Z= 0.346 Angle : 1.005 11.983 5782 Z= 0.659 Chirality : 0.086 1.215 678 Planarity : 0.019 0.294 700 Dihedral : 17.751 105.346 1494 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.17 % Allowed : 13.98 % Favored : 83.86 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.31), residues: 539 helix: -0.93 (0.25), residues: 333 sheet: None (None), residues: 0 loop : -2.71 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 171 HIS 0.002 0.001 HIS A 575 PHE 0.012 0.001 PHE A 621 TYR 0.026 0.002 TYR A 625 ARG 0.002 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.426 Fit side-chains REVERT: A 198 ASP cc_start: 0.8666 (m-30) cc_final: 0.8031 (m-30) REVERT: A 253 ARG cc_start: 0.7701 (mtm180) cc_final: 0.6301 (mtp-110) REVERT: A 580 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7566 (mtt90) REVERT: A 623 ARG cc_start: 0.7437 (tpp80) cc_final: 0.7188 (mtm-85) REVERT: A 648 LYS cc_start: 0.7736 (ttmt) cc_final: 0.6993 (ttpt) outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 1.0495 time to fit residues: 90.5234 Evaluate side-chains 59 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 563 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 0.0770 chunk 13 optimal weight: 0.3980 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.0060 chunk 49 optimal weight: 6.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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: 0.7773 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4258 Z= 0.174 Angle : 0.637 8.399 5782 Z= 0.312 Chirality : 0.054 0.736 678 Planarity : 0.004 0.045 700 Dihedral : 8.937 54.549 662 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.89 % Allowed : 20.00 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.36), residues: 539 helix: 0.83 (0.29), residues: 342 sheet: None (None), residues: 0 loop : -2.20 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 171 HIS 0.002 0.001 HIS A 115 PHE 0.011 0.001 PHE A 501 TYR 0.021 0.001 TYR A 625 ARG 0.002 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.422 Fit side-chains REVERT: A 198 ASP cc_start: 0.8586 (m-30) cc_final: 0.7983 (m-30) REVERT: A 253 ARG cc_start: 0.7707 (mtm180) cc_final: 0.6322 (mtp-110) REVERT: A 348 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7586 (tp-100) REVERT: A 648 LYS cc_start: 0.7656 (ttmt) cc_final: 0.7074 (ttpt) outliers start: 12 outliers final: 6 residues processed: 63 average time/residue: 1.0255 time to fit residues: 67.3206 Evaluate side-chains 54 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7890 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4258 Z= 0.263 Angle : 0.620 9.317 5782 Z= 0.314 Chirality : 0.053 0.676 678 Planarity : 0.004 0.044 700 Dihedral : 7.182 59.366 660 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.41 % Allowed : 20.24 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.37), residues: 539 helix: 1.31 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.85 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 258 HIS 0.002 0.001 HIS A 520 PHE 0.017 0.001 PHE A 621 TYR 0.025 0.002 TYR A 625 ARG 0.002 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.506 Fit side-chains REVERT: A 96 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8301 (mt) REVERT: A 198 ASP cc_start: 0.8721 (m-30) cc_final: 0.8075 (m-30) REVERT: A 251 ASP cc_start: 0.7008 (m-30) cc_final: 0.6699 (m-30) REVERT: A 253 ARG cc_start: 0.7750 (mtm180) cc_final: 0.6293 (mtp-110) REVERT: A 348 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7728 (tp-100) REVERT: A 623 ARG cc_start: 0.7502 (tpp80) cc_final: 0.7228 (mtm-85) REVERT: A 648 LYS cc_start: 0.7851 (ttmt) cc_final: 0.7259 (ttpt) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 1.1759 time to fit residues: 69.6939 Evaluate side-chains 54 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 647 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7907 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4258 Z= 0.245 Angle : 0.573 7.544 5782 Z= 0.297 Chirality : 0.050 0.628 678 Planarity : 0.004 0.046 700 Dihedral : 6.670 54.183 660 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.61 % Allowed : 19.28 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.37), residues: 539 helix: 1.57 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -1.68 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 171 HIS 0.002 0.001 HIS A 520 PHE 0.019 0.001 PHE A 621 TYR 0.022 0.002 TYR A 625 ARG 0.002 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 0.461 Fit side-chains REVERT: A 96 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8280 (mt) REVERT: A 198 ASP cc_start: 0.8710 (m-30) cc_final: 0.8064 (m-30) REVERT: A 251 ASP cc_start: 0.6996 (m-30) cc_final: 0.6703 (m-30) REVERT: A 348 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7686 (tp-100) REVERT: A 623 ARG cc_start: 0.7502 (tpp80) cc_final: 0.7219 (mtt-85) REVERT: A 640 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.7767 (t80) REVERT: A 648 LYS cc_start: 0.7779 (ttmt) cc_final: 0.7208 (ttpt) outliers start: 15 outliers final: 6 residues processed: 61 average time/residue: 1.0192 time to fit residues: 64.9353 Evaluate side-chains 55 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 647 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.0370 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 0.0020 chunk 46 optimal weight: 0.2980 chunk 13 optimal weight: 0.3980 chunk 17 optimal weight: 0.0670 chunk 47 optimal weight: 1.9990 overall best weight: 0.1604 ------------------------------------------------------------------------------- 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: 0.7771 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4258 Z= 0.134 Angle : 0.501 7.026 5782 Z= 0.253 Chirality : 0.047 0.598 678 Planarity : 0.004 0.048 700 Dihedral : 6.326 53.427 660 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.89 % Allowed : 20.96 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.37), residues: 539 helix: 2.26 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -1.67 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 258 HIS 0.001 0.000 HIS A 115 PHE 0.012 0.001 PHE A 501 TYR 0.019 0.001 TYR A 590 ARG 0.001 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.462 Fit side-chains REVERT: A 198 ASP cc_start: 0.8620 (m-30) cc_final: 0.7969 (m-30) REVERT: A 253 ARG cc_start: 0.7778 (mtm180) cc_final: 0.6376 (mtp-110) REVERT: A 348 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7456 (tp-100) REVERT: A 392 LEU cc_start: 0.8479 (mt) cc_final: 0.8272 (mt) REVERT: A 417 MET cc_start: 0.8503 (tpp) cc_final: 0.8229 (mmm) outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 1.0407 time to fit residues: 61.9843 Evaluate side-chains 57 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 50 optimal weight: 0.0170 chunk 5 optimal weight: 0.5980 overall best weight: 0.6620 ------------------------------------------------------------------------------- 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: 0.7850 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4258 Z= 0.185 Angle : 0.535 7.980 5782 Z= 0.273 Chirality : 0.048 0.596 678 Planarity : 0.004 0.046 700 Dihedral : 6.289 53.713 660 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.17 % Allowed : 22.41 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.37), residues: 539 helix: 2.21 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -1.50 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.002 0.001 HIS A 575 PHE 0.013 0.001 PHE A 621 TYR 0.023 0.001 TYR A 625 ARG 0.002 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.461 Fit side-chains REVERT: A 81 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7736 (tp) REVERT: A 198 ASP cc_start: 0.8676 (m-30) cc_final: 0.7998 (m-30) REVERT: A 253 ARG cc_start: 0.7783 (mtm180) cc_final: 0.6400 (mtp-110) REVERT: A 348 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7597 (tp-100) REVERT: A 417 MET cc_start: 0.8538 (tpp) cc_final: 0.8274 (mmm) REVERT: A 623 ARG cc_start: 0.7313 (tpp80) cc_final: 0.7062 (mtt180) REVERT: A 648 LYS cc_start: 0.7391 (ttmt) cc_final: 0.6867 (ttpt) outliers start: 9 outliers final: 5 residues processed: 54 average time/residue: 1.2432 time to fit residues: 69.7505 Evaluate side-chains 55 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 507 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.0770 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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: 0.7836 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4258 Z= 0.163 Angle : 0.512 7.748 5782 Z= 0.260 Chirality : 0.047 0.591 678 Planarity : 0.004 0.045 700 Dihedral : 6.137 53.778 659 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.65 % Allowed : 22.17 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.37), residues: 539 helix: 2.32 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -1.38 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.001 0.001 HIS A 520 PHE 0.013 0.001 PHE A 386 TYR 0.021 0.001 TYR A 625 ARG 0.001 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.466 Fit side-chains REVERT: A 81 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7726 (tp) REVERT: A 198 ASP cc_start: 0.8681 (m-30) cc_final: 0.8020 (m-30) REVERT: A 253 ARG cc_start: 0.7801 (mtm180) cc_final: 0.6405 (mtp-110) REVERT: A 348 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7588 (tp-100) REVERT: A 417 MET cc_start: 0.8544 (tpp) cc_final: 0.8263 (mmm) REVERT: A 623 ARG cc_start: 0.7289 (tpp80) cc_final: 0.7053 (mtt180) REVERT: A 648 LYS cc_start: 0.7295 (ttmt) cc_final: 0.6813 (ttpt) outliers start: 11 outliers final: 6 residues processed: 55 average time/residue: 1.1604 time to fit residues: 66.4818 Evaluate side-chains 55 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 558 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.0170 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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: 0.7854 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4258 Z= 0.182 Angle : 0.527 8.740 5782 Z= 0.268 Chirality : 0.047 0.591 678 Planarity : 0.004 0.044 700 Dihedral : 6.128 53.811 659 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.65 % Allowed : 22.17 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.37), residues: 539 helix: 2.32 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -1.38 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 254 HIS 0.001 0.001 HIS A 520 PHE 0.015 0.001 PHE A 386 TYR 0.022 0.001 TYR A 625 ARG 0.002 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.465 Fit side-chains REVERT: A 81 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7715 (tp) REVERT: A 198 ASP cc_start: 0.8670 (m-30) cc_final: 0.8012 (m-30) REVERT: A 348 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7615 (tp-100) REVERT: A 417 MET cc_start: 0.8538 (tpp) cc_final: 0.8265 (mmm) REVERT: A 623 ARG cc_start: 0.7313 (tpp80) cc_final: 0.7070 (mtt180) REVERT: A 648 LYS cc_start: 0.7365 (ttmt) cc_final: 0.6857 (ttpt) outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 1.1432 time to fit residues: 64.1808 Evaluate side-chains 57 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 558 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4258 Z= 0.167 Angle : 0.515 8.947 5782 Z= 0.261 Chirality : 0.047 0.586 678 Planarity : 0.004 0.043 700 Dihedral : 6.056 53.706 659 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.41 % Allowed : 21.93 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.37), residues: 539 helix: 2.40 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -1.35 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.002 0.001 HIS A 520 PHE 0.016 0.001 PHE A 386 TYR 0.021 0.001 TYR A 625 ARG 0.001 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.459 Fit side-chains REVERT: A 81 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7731 (tp) REVERT: A 198 ASP cc_start: 0.8686 (m-30) cc_final: 0.8021 (m-30) REVERT: A 348 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7605 (tp-100) REVERT: A 417 MET cc_start: 0.8470 (tpp) cc_final: 0.8193 (mmm) REVERT: A 623 ARG cc_start: 0.7293 (tpp80) cc_final: 0.7065 (mtt180) REVERT: A 648 LYS cc_start: 0.7326 (ttmt) cc_final: 0.6816 (ttpt) outliers start: 10 outliers final: 6 residues processed: 56 average time/residue: 1.1424 time to fit residues: 66.5733 Evaluate side-chains 56 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 507 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 0.0370 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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: 0.7838 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4258 Z= 0.167 Angle : 0.523 9.137 5782 Z= 0.267 Chirality : 0.047 0.585 678 Planarity : 0.004 0.044 700 Dihedral : 6.027 53.471 659 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.17 % Allowed : 21.93 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.37), residues: 539 helix: 2.34 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -1.39 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 254 HIS 0.001 0.001 HIS A 520 PHE 0.017 0.001 PHE A 386 TYR 0.021 0.001 TYR A 625 ARG 0.001 0.000 ARG A 633 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.425 Fit side-chains REVERT: A 81 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7703 (tp) REVERT: A 198 ASP cc_start: 0.8678 (m-30) cc_final: 0.8022 (m-30) REVERT: A 348 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7607 (tp-100) REVERT: A 417 MET cc_start: 0.8448 (tpp) cc_final: 0.8174 (mmm) REVERT: A 605 ASN cc_start: 0.7228 (t0) cc_final: 0.7026 (p0) REVERT: A 623 ARG cc_start: 0.7292 (tpp80) cc_final: 0.7077 (mtt180) REVERT: A 648 LYS cc_start: 0.7295 (ttmt) cc_final: 0.6797 (ttpt) outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 1.1768 time to fit residues: 67.3676 Evaluate side-chains 56 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 507 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.0570 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.153490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114584 restraints weight = 4988.453| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.40 r_work: 0.3161 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4258 Z= 0.156 Angle : 0.510 9.165 5782 Z= 0.259 Chirality : 0.046 0.577 678 Planarity : 0.004 0.045 700 Dihedral : 5.961 53.435 659 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.69 % Allowed : 22.41 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.37), residues: 539 helix: 2.38 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -1.31 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.001 0.001 HIS A 520 PHE 0.017 0.001 PHE A 386 TYR 0.021 0.001 TYR A 625 ARG 0.002 0.000 ARG A 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1831.30 seconds wall clock time: 34 minutes 1.61 seconds (2041.61 seconds total)