Starting phenix.real_space_refine on Tue Feb 13 09:02:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdh_34673/02_2024/8hdh_34673_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdh_34673/02_2024/8hdh_34673.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdh_34673/02_2024/8hdh_34673_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdh_34673/02_2024/8hdh_34673_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdh_34673/02_2024/8hdh_34673_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdh_34673/02_2024/8hdh_34673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdh_34673/02_2024/8hdh_34673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdh_34673/02_2024/8hdh_34673_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdh_34673/02_2024/8hdh_34673_updated.pdb" } 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= 0.006 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 S 38 5.16 5 Na 1 4.78 5 C 3153 2.51 5 N 776 2.21 5 O 809 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A ARG 651": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4778 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4497 Classifications: {'peptide': 586} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 558} Chain breaks: 1 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 50 Unusual residues: {' NA': 1, 'L3R': 1, 'NAG': 1} Classifications: {'undetermined': 3, 'water': 4} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.34, per 1000 atoms: 0.70 Number of scatterers: 4778 At special positions: 0 Unit cell: (75, 76, 93, 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 38 16.00 Na 1 11.00 F 1 9.00 O 809 8.00 N 776 7.00 C 3153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.28 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.36 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.24 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.39 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: 1.86 Conformation dependent library (CDL) restraints added in 841.4 milliseconds 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1116 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 0 sheets defined 74.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 23 through 46 Processing helix chain 'A' and resid 52 through 60 removed outlier: 6.948A pdb=" N GLY A 59 " --> pdb=" O TYR A 55 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ARG A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 94 through 111 removed outlier: 3.746A pdb=" N ASN A 101 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP A 111 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 120 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 137 through 153 Processing helix chain 'A' and resid 155 through 169 Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 194 through 223 removed outlier: 3.523A pdb=" N VAL A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.541A pdb=" N PHE A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 276 through 292 Processing helix chain 'A' and resid 295 through 302 removed outlier: 4.484A pdb=" N ARG A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 327 removed outlier: 3.838A pdb=" N THR A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 348 through 355 Processing helix chain 'A' and resid 362 through 373 removed outlier: 4.398A pdb=" N TYR A 366 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Proline residue: A 367 - end of helix removed outlier: 3.986A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 372 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 408 Processing helix chain 'A' and resid 410 through 413 No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 421 through 445 removed outlier: 3.540A pdb=" N VAL A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 449 through 476 removed outlier: 4.190A pdb=" N LEU A 452 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 453 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 459 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER A 460 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 463 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) Proline residue: A 465 - end of helix removed outlier: 3.696A pdb=" N PHE A 471 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 474 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 500 removed outlier: 3.695A pdb=" N ARG A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 519 through 522 No H-bonds generated for 'chain 'A' and resid 519 through 522' Processing helix chain 'A' and resid 526 through 547 removed outlier: 3.671A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 555 No H-bonds generated for 'chain 'A' and resid 553 through 555' Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 647 through 670 Processing helix chain 'B' and resid 29 through 54 295 hydrogen bonds defined for protein. 810 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: 1.27 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 703 1.29 - 1.43: 1387 1.43 - 1.57: 2754 1.57 - 1.71: 0 1.71 - 1.85: 59 Bond restraints: 4903 Sorted by residual: bond pdb=" C18 L3R A 802 " pdb=" C2 L3R A 802 " ideal model delta sigma weight residual 1.597 1.416 0.181 2.00e-02 2.50e+03 8.16e+01 bond pdb=" C17 L3R A 802 " pdb=" S1 L3R A 802 " ideal model delta sigma weight residual 1.556 1.718 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" C1 L3R A 802 " pdb=" S1 L3R A 802 " ideal model delta sigma weight residual 1.555 1.712 -0.157 2.00e-02 2.50e+03 6.16e+01 bond pdb=" C LEU A 497 " pdb=" O LEU A 497 " ideal model delta sigma weight residual 1.236 1.152 0.085 1.32e-02 5.74e+03 4.12e+01 bond pdb=" C PHE A 98 " pdb=" O PHE A 98 " ideal model delta sigma weight residual 1.236 1.303 -0.066 1.15e-02 7.56e+03 3.30e+01 ... (remaining 4898 not shown) Histogram of bond angle deviations from ideal: 90.90 - 99.70: 11 99.70 - 108.50: 490 108.50 - 117.29: 3071 117.29 - 126.09: 2962 126.09 - 134.89: 155 Bond angle restraints: 6689 Sorted by residual: angle pdb=" C10 L3R A 802 " pdb=" C1 L3R A 802 " pdb=" S1 L3R A 802 " ideal model delta sigma weight residual 162.47 116.29 46.18 3.00e+00 1.11e-01 2.37e+02 angle pdb=" C10 L3R A 802 " pdb=" C1 L3R A 802 " pdb=" C2 L3R A 802 " ideal model delta sigma weight residual 86.88 130.23 -43.35 3.00e+00 1.11e-01 2.09e+02 angle pdb=" CA PHE A 520 " pdb=" CB PHE A 520 " pdb=" CG PHE A 520 " ideal model delta sigma weight residual 113.80 104.85 8.95 1.00e+00 1.00e+00 8.01e+01 angle pdb=" CA PHE A 520 " pdb=" C PHE A 520 " pdb=" O PHE A 520 " ideal model delta sigma weight residual 119.97 111.62 8.35 1.15e+00 7.56e-01 5.27e+01 angle pdb=" C LEU A 182 " pdb=" N GLY A 183 " pdb=" CA GLY A 183 " ideal model delta sigma weight residual 119.94 127.85 -7.91 1.09e+00 8.42e-01 5.27e+01 ... (remaining 6684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 2520 15.85 - 31.70: 225 31.70 - 47.55: 63 47.55 - 63.40: 14 63.40 - 79.24: 6 Dihedral angle restraints: 2828 sinusoidal: 1076 harmonic: 1752 Sorted by residual: dihedral pdb=" CB CYS A 255 " pdb=" SG CYS A 255 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual -86.00 -30.53 -55.47 1 1.00e+01 1.00e-02 4.16e+01 dihedral pdb=" CA ARG A 136 " pdb=" C ARG A 136 " pdb=" N ARG A 137 " pdb=" CA ARG A 137 " ideal model delta harmonic sigma weight residual 180.00 -150.72 -29.28 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ALA A 247 " pdb=" C ALA A 247 " pdb=" N VAL A 248 " pdb=" CA VAL A 248 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 2825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 380 0.064 - 0.127: 252 0.127 - 0.191: 119 0.191 - 0.255: 22 0.255 - 0.318: 5 Chirality restraints: 778 Sorted by residual: chirality pdb=" CB VAL A 434 " pdb=" CA VAL A 434 " pdb=" CG1 VAL A 434 " pdb=" CG2 VAL A 434 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA ILE A 251 " pdb=" N ILE A 251 " pdb=" C ILE A 251 " pdb=" CB ILE A 251 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA ILE A 501 " pdb=" N ILE A 501 " pdb=" C ILE A 501 " pdb=" CB ILE A 501 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 775 not shown) Planarity restraints: 818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 L3R A 802 " 0.023 2.00e-02 2.50e+03 8.68e-02 1.32e+02 pdb=" C10 L3R A 802 " -0.127 2.00e-02 2.50e+03 pdb=" C17 L3R A 802 " 0.002 2.00e-02 2.50e+03 pdb=" C18 L3R A 802 " -0.061 2.00e-02 2.50e+03 pdb=" C19 L3R A 802 " -0.070 2.00e-02 2.50e+03 pdb=" C2 L3R A 802 " 0.108 2.00e-02 2.50e+03 pdb=" S1 L3R A 802 " 0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 801 " -0.105 2.00e-02 2.50e+03 8.66e-02 9.37e+01 pdb=" C7 NAG A 801 " 0.029 2.00e-02 2.50e+03 pdb=" C8 NAG A 801 " -0.079 2.00e-02 2.50e+03 pdb=" N2 NAG A 801 " 0.137 2.00e-02 2.50e+03 pdb=" O7 NAG A 801 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 502 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C PRO A 502 " -0.068 2.00e-02 2.50e+03 pdb=" O PRO A 502 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU A 503 " 0.024 2.00e-02 2.50e+03 ... (remaining 815 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 37 2.61 - 3.18: 4083 3.18 - 3.75: 7676 3.75 - 4.33: 10907 4.33 - 4.90: 17652 Nonbonded interactions: 40355 Sorted by model distance: nonbonded pdb=" O ALA A 73 " pdb="NA NA A 803 " model vdw 2.036 2.470 nonbonded pdb=" OG SER A 393 " pdb="NA NA A 803 " model vdw 2.260 2.470 nonbonded pdb=" ND2 ASN A 250 " pdb=" C1 NAG A 801 " model vdw 2.283 3.550 nonbonded pdb=" O MET A 407 " pdb=" OG1 THR A 411 " model vdw 2.314 2.440 nonbonded pdb=" O GLY A 332 " pdb=" OG SER A 335 " model vdw 2.332 2.440 ... (remaining 40350 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: 0.110 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: 0.700 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.170 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.017 0.181 4903 Z= 1.081 Angle : 2.354 46.182 6689 Z= 1.661 Chirality : 0.094 0.318 778 Planarity : 0.007 0.103 818 Dihedral : 14.150 79.244 1700 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.49 % Allowed : 3.94 % Favored : 95.57 % Rotamer: Outliers : 1.00 % Allowed : 8.00 % Favored : 91.00 % Cbeta Deviations : 0.18 % 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: -2.42 (0.30), residues: 609 helix: -1.47 (0.20), residues: 442 sheet: None (None), residues: 0 loop : -1.43 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 65 HIS 0.007 0.002 HIS A 80 PHE 0.028 0.004 PHE A 520 TYR 0.021 0.004 TYR A 233 ARG 0.006 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.540 Fit side-chains REVERT: A 46 ARG cc_start: 0.5535 (ttt90) cc_final: 0.4409 (mmp80) REVERT: A 62 MET cc_start: 0.9096 (mmp) cc_final: 0.8808 (mmp) REVERT: A 104 PHE cc_start: 0.7000 (m-80) cc_final: 0.6434 (t80) REVERT: A 306 SER cc_start: 0.6640 (t) cc_final: 0.6392 (p) REVERT: A 308 THR cc_start: 0.7973 (t) cc_final: 0.7696 (m) REVERT: A 353 ARG cc_start: 0.7351 (ttp-110) cc_final: 0.7061 (ttm110) REVERT: A 359 VAL cc_start: 0.8251 (m) cc_final: 0.7949 (t) REVERT: A 372 LYS cc_start: 0.7916 (mmtm) cc_final: 0.7663 (mmmt) REVERT: A 412 ARG cc_start: 0.6615 (ttt90) cc_final: 0.5746 (ttt180) REVERT: A 504 PHE cc_start: 0.6786 (t80) cc_final: 0.6420 (m-80) REVERT: A 558 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7602 (mtm180) REVERT: A 645 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7001 (mt-10) REVERT: A 651 ARG cc_start: 0.6534 (ttm110) cc_final: 0.5905 (tpt170) REVERT: A 661 MET cc_start: 0.7137 (mtt) cc_final: 0.6892 (tpt) REVERT: B 31 MET cc_start: 0.5863 (ptm) cc_final: 0.5476 (mtt) outliers start: 5 outliers final: 1 residues processed: 109 average time/residue: 0.1904 time to fit residues: 25.8151 Evaluate side-chains 77 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 0.0020 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 399 ASN A 557 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4903 Z= 0.189 Angle : 0.605 7.002 6689 Z= 0.315 Chirality : 0.042 0.143 778 Planarity : 0.004 0.035 818 Dihedral : 6.513 84.836 697 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.60 % Allowed : 10.20 % Favored : 88.20 % 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: 0.54 (0.33), residues: 609 helix: 0.85 (0.24), residues: 449 sheet: None (None), residues: 0 loop : -0.85 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 65 HIS 0.004 0.001 HIS A 557 PHE 0.009 0.001 PHE A 486 TYR 0.014 0.002 TYR A 256 ARG 0.003 0.000 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.558 Fit side-chains REVERT: A 46 ARG cc_start: 0.5363 (ttt90) cc_final: 0.4998 (ttm-80) REVERT: A 62 MET cc_start: 0.9006 (mmp) cc_final: 0.8767 (mmp) REVERT: A 353 ARG cc_start: 0.7111 (ttp-110) cc_final: 0.6868 (mtm110) REVERT: A 359 VAL cc_start: 0.8107 (m) cc_final: 0.7895 (p) REVERT: A 372 LYS cc_start: 0.7842 (mmtm) cc_final: 0.7614 (mmmm) REVERT: A 374 MET cc_start: 0.8379 (mmm) cc_final: 0.8172 (mmp) REVERT: A 412 ARG cc_start: 0.6229 (ttt90) cc_final: 0.5408 (ttt180) REVERT: A 421 GLU cc_start: 0.6974 (tt0) cc_final: 0.6487 (tt0) REVERT: A 651 ARG cc_start: 0.6380 (ttm110) cc_final: 0.5809 (tpt170) REVERT: B 31 MET cc_start: 0.5397 (ptm) cc_final: 0.5079 (mtt) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.1979 time to fit residues: 22.2023 Evaluate side-chains 72 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4903 Z= 0.141 Angle : 0.526 6.644 6689 Z= 0.269 Chirality : 0.039 0.141 778 Planarity : 0.004 0.038 818 Dihedral : 5.822 81.898 697 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.60 % Allowed : 12.60 % Favored : 84.80 % 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: 1.48 (0.35), residues: 609 helix: 1.58 (0.25), residues: 446 sheet: None (None), residues: 0 loop : -0.62 (0.52), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 440 HIS 0.001 0.000 HIS A 80 PHE 0.008 0.001 PHE A 520 TYR 0.011 0.001 TYR A 256 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.532 Fit side-chains REVERT: A 46 ARG cc_start: 0.5631 (ttt90) cc_final: 0.4326 (mmp80) REVERT: A 104 PHE cc_start: 0.6670 (m-80) cc_final: 0.6061 (t80) REVERT: A 353 ARG cc_start: 0.7074 (ttp-110) cc_final: 0.6843 (mtm110) REVERT: A 412 ARG cc_start: 0.6255 (ttt90) cc_final: 0.5404 (ttt180) REVERT: A 505 SER cc_start: 0.8080 (OUTLIER) cc_final: 0.7838 (p) REVERT: A 651 ARG cc_start: 0.6487 (ttm110) cc_final: 0.5913 (tpt170) REVERT: B 31 MET cc_start: 0.5405 (ptm) cc_final: 0.5072 (mtt) outliers start: 13 outliers final: 8 residues processed: 81 average time/residue: 0.2180 time to fit residues: 21.7583 Evaluate side-chains 71 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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: 0.7226 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4903 Z= 0.190 Angle : 0.546 7.635 6689 Z= 0.279 Chirality : 0.041 0.148 778 Planarity : 0.004 0.037 818 Dihedral : 5.904 84.217 697 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.00 % Allowed : 14.00 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.35), residues: 609 helix: 1.58 (0.25), residues: 444 sheet: None (None), residues: 0 loop : -0.34 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 440 HIS 0.003 0.001 HIS A 80 PHE 0.010 0.001 PHE A 476 TYR 0.013 0.001 TYR A 128 ARG 0.001 0.000 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.483 Fit side-chains REVERT: A 36 VAL cc_start: 0.7092 (t) cc_final: 0.6891 (t) REVERT: A 46 ARG cc_start: 0.5626 (ttt90) cc_final: 0.5149 (ttm-80) REVERT: A 104 PHE cc_start: 0.6308 (m-80) cc_final: 0.5733 (t80) REVERT: A 353 ARG cc_start: 0.7078 (ttp-110) cc_final: 0.6862 (ttm110) REVERT: A 359 VAL cc_start: 0.8090 (m) cc_final: 0.7888 (p) REVERT: A 412 ARG cc_start: 0.6109 (ttt90) cc_final: 0.5336 (ttt180) REVERT: A 421 GLU cc_start: 0.7035 (tt0) cc_final: 0.6524 (tt0) REVERT: A 548 THR cc_start: 0.6624 (OUTLIER) cc_final: 0.6136 (p) REVERT: A 651 ARG cc_start: 0.6456 (ttm110) cc_final: 0.5850 (tpt170) REVERT: B 31 MET cc_start: 0.5417 (ptm) cc_final: 0.5064 (mtt) outliers start: 10 outliers final: 6 residues processed: 78 average time/residue: 0.2130 time to fit residues: 20.8101 Evaluate side-chains 74 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 0.0170 overall best weight: 1.1422 ------------------------------------------------------------------------------- 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: 0.7209 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4903 Z= 0.154 Angle : 0.497 6.646 6689 Z= 0.255 Chirality : 0.039 0.147 778 Planarity : 0.004 0.036 818 Dihedral : 5.722 83.966 697 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.00 % Allowed : 14.40 % Favored : 83.60 % 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: 1.63 (0.35), residues: 609 helix: 1.64 (0.25), residues: 448 sheet: None (None), residues: 0 loop : -0.41 (0.54), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 440 HIS 0.002 0.001 HIS A 80 PHE 0.007 0.001 PHE A 476 TYR 0.011 0.001 TYR A 128 ARG 0.001 0.000 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.567 Fit side-chains REVERT: A 36 VAL cc_start: 0.7016 (t) cc_final: 0.6799 (t) REVERT: A 46 ARG cc_start: 0.5584 (ttt90) cc_final: 0.4300 (mmp80) REVERT: A 104 PHE cc_start: 0.6446 (m-80) cc_final: 0.5873 (t80) REVERT: A 412 ARG cc_start: 0.6111 (ttt90) cc_final: 0.5363 (ttt180) REVERT: A 651 ARG cc_start: 0.6459 (ttm110) cc_final: 0.5850 (tpt170) REVERT: B 31 MET cc_start: 0.5325 (ptm) cc_final: 0.4974 (mtt) outliers start: 10 outliers final: 7 residues processed: 72 average time/residue: 0.1929 time to fit residues: 17.5942 Evaluate side-chains 65 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 0.4980 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.7189 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4903 Z= 0.138 Angle : 0.482 6.583 6689 Z= 0.246 Chirality : 0.039 0.146 778 Planarity : 0.004 0.035 818 Dihedral : 5.613 83.941 697 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.40 % Allowed : 15.20 % Favored : 82.40 % 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: 1.72 (0.35), residues: 609 helix: 1.69 (0.25), residues: 447 sheet: None (None), residues: 0 loop : -0.33 (0.54), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 440 HIS 0.002 0.000 HIS A 80 PHE 0.009 0.001 PHE A 520 TYR 0.009 0.001 TYR A 128 ARG 0.001 0.000 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.491 Fit side-chains REVERT: A 46 ARG cc_start: 0.5644 (ttt90) cc_final: 0.4433 (mmp80) REVERT: A 104 PHE cc_start: 0.6127 (m-80) cc_final: 0.5565 (t80) REVERT: A 412 ARG cc_start: 0.6051 (ttt90) cc_final: 0.5304 (ttt180) REVERT: A 421 GLU cc_start: 0.6855 (tt0) cc_final: 0.6349 (tt0) REVERT: A 651 ARG cc_start: 0.6454 (ttm110) cc_final: 0.5844 (tpt170) REVERT: B 31 MET cc_start: 0.5307 (ptm) cc_final: 0.4954 (mtt) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 0.1743 time to fit residues: 16.7969 Evaluate side-chains 68 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 0.0070 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4903 Z= 0.197 Angle : 0.518 6.703 6689 Z= 0.265 Chirality : 0.040 0.150 778 Planarity : 0.004 0.036 818 Dihedral : 5.852 84.904 697 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.40 % Allowed : 16.00 % Favored : 81.60 % 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 (0.35), residues: 609 helix: 1.55 (0.25), residues: 447 sheet: None (None), residues: 0 loop : -0.31 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 429 HIS 0.003 0.001 HIS A 80 PHE 0.009 0.001 PHE A 476 TYR 0.009 0.001 TYR A 128 ARG 0.002 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.562 Fit side-chains REVERT: A 46 ARG cc_start: 0.5563 (ttt90) cc_final: 0.4271 (mmp80) REVERT: A 103 LEU cc_start: 0.7303 (tt) cc_final: 0.7095 (mp) REVERT: A 104 PHE cc_start: 0.6405 (m-80) cc_final: 0.5757 (t80) REVERT: A 321 LYS cc_start: 0.8019 (mmmm) cc_final: 0.7774 (mtpp) REVERT: A 412 ARG cc_start: 0.6112 (ttt90) cc_final: 0.5453 (ttt180) REVERT: A 421 GLU cc_start: 0.6998 (tt0) cc_final: 0.6496 (tt0) REVERT: A 651 ARG cc_start: 0.6447 (ttm110) cc_final: 0.5808 (mmt180) REVERT: B 31 MET cc_start: 0.5303 (ptm) cc_final: 0.4954 (mtt) outliers start: 12 outliers final: 9 residues processed: 77 average time/residue: 0.1962 time to fit residues: 19.1973 Evaluate side-chains 73 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 0.0870 chunk 42 optimal weight: 0.2980 chunk 16 optimal weight: 0.0770 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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: 0.7175 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4903 Z= 0.129 Angle : 0.472 6.511 6689 Z= 0.241 Chirality : 0.038 0.144 778 Planarity : 0.004 0.036 818 Dihedral : 5.552 84.415 697 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.80 % Allowed : 15.80 % Favored : 82.40 % 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: 1.83 (0.36), residues: 609 helix: 1.77 (0.25), residues: 446 sheet: None (None), residues: 0 loop : -0.28 (0.54), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 65 HIS 0.001 0.000 HIS A 80 PHE 0.008 0.001 PHE A 520 TYR 0.008 0.001 TYR A 256 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.533 Fit side-chains REVERT: A 46 ARG cc_start: 0.5700 (ttt90) cc_final: 0.4472 (mmp80) REVERT: A 104 PHE cc_start: 0.6227 (m-80) cc_final: 0.5595 (t80) REVERT: A 412 ARG cc_start: 0.6174 (ttt90) cc_final: 0.5503 (ttt180) REVERT: A 421 GLU cc_start: 0.6844 (tt0) cc_final: 0.6309 (tt0) REVERT: A 651 ARG cc_start: 0.6419 (ttm110) cc_final: 0.5780 (mmt180) REVERT: B 31 MET cc_start: 0.5299 (ptm) cc_final: 0.4944 (mtt) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.1875 time to fit residues: 16.9255 Evaluate side-chains 69 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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: 0.7269 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4903 Z= 0.314 Angle : 0.594 6.971 6689 Z= 0.307 Chirality : 0.044 0.159 778 Planarity : 0.005 0.035 818 Dihedral : 6.226 85.972 697 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.00 % Allowed : 14.60 % Favored : 83.40 % 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: 1.23 (0.35), residues: 609 helix: 1.30 (0.24), residues: 444 sheet: None (None), residues: 0 loop : -0.38 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 429 HIS 0.002 0.001 HIS A 565 PHE 0.012 0.001 PHE A 476 TYR 0.015 0.002 TYR A 526 ARG 0.002 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.531 Fit side-chains REVERT: A 104 PHE cc_start: 0.6506 (m-80) cc_final: 0.5793 (t80) REVERT: A 412 ARG cc_start: 0.6098 (ttt90) cc_final: 0.5460 (ttt180) REVERT: A 421 GLU cc_start: 0.6907 (tt0) cc_final: 0.6390 (tt0) REVERT: A 548 THR cc_start: 0.6595 (OUTLIER) cc_final: 0.6112 (p) REVERT: A 651 ARG cc_start: 0.6536 (ttm110) cc_final: 0.5887 (mmt180) REVERT: A 661 MET cc_start: 0.7426 (tpt) cc_final: 0.7220 (tpt) REVERT: B 31 MET cc_start: 0.5333 (ptm) cc_final: 0.4942 (mtt) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.1849 time to fit residues: 17.4692 Evaluate side-chains 72 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 548 THR 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: 6.9990 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.7219 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4903 Z= 0.161 Angle : 0.499 6.632 6689 Z= 0.256 Chirality : 0.039 0.148 778 Planarity : 0.004 0.035 818 Dihedral : 5.904 85.004 697 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.60 % Allowed : 15.60 % Favored : 82.80 % 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: 1.44 (0.35), residues: 609 helix: 1.46 (0.25), residues: 446 sheet: None (None), residues: 0 loop : -0.34 (0.54), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 276 HIS 0.002 0.001 HIS A 80 PHE 0.008 0.001 PHE A 476 TYR 0.008 0.001 TYR A 128 ARG 0.001 0.000 ARG A 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.529 Fit side-chains REVERT: A 104 PHE cc_start: 0.6518 (m-80) cc_final: 0.5754 (t80) REVERT: A 125 MET cc_start: 0.8293 (mmp) cc_final: 0.8070 (mmp) REVERT: A 412 ARG cc_start: 0.6094 (ttt90) cc_final: 0.5457 (ttt180) REVERT: A 421 GLU cc_start: 0.6798 (tt0) cc_final: 0.6285 (tt0) REVERT: A 548 THR cc_start: 0.6518 (OUTLIER) cc_final: 0.6041 (p) REVERT: A 651 ARG cc_start: 0.6444 (ttm110) cc_final: 0.5810 (mmt180) REVERT: B 31 MET cc_start: 0.5381 (ptm) cc_final: 0.4995 (mtt) outliers start: 8 outliers final: 7 residues processed: 69 average time/residue: 0.1824 time to fit residues: 16.1700 Evaluate side-chains 72 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 0.0270 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.131021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.110315 restraints weight = 5370.398| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.47 r_work: 0.3086 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4903 Z= 0.164 Angle : 0.497 6.627 6689 Z= 0.255 Chirality : 0.039 0.147 778 Planarity : 0.004 0.035 818 Dihedral : 5.793 84.531 697 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.00 % Allowed : 15.00 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.35), residues: 609 helix: 1.54 (0.25), residues: 446 sheet: None (None), residues: 0 loop : -0.33 (0.54), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 429 HIS 0.002 0.001 HIS A 80 PHE 0.007 0.001 PHE A 476 TYR 0.007 0.001 TYR A 128 ARG 0.001 0.000 ARG A 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1412.97 seconds wall clock time: 26 minutes 5.00 seconds (1565.00 seconds total)