Starting phenix.real_space_refine on Tue Feb 13 08:30:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/02_2024/8bvt_16271_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/02_2024/8bvt_16271.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/02_2024/8bvt_16271_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/02_2024/8bvt_16271_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/02_2024/8bvt_16271_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/02_2024/8bvt_16271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/02_2024/8bvt_16271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/02_2024/8bvt_16271_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/02_2024/8bvt_16271_updated.pdb" } resolution = 3.94 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= 0.002 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 2907 2.51 5 N 776 2.21 5 O 801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4517 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3933 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 28, 'TRANS': 479} Chain breaks: 2 Chain: "B" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 565 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 462 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 5, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 216 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'RTO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.10, per 1000 atoms: 0.69 Number of scatterers: 4517 At special positions: 0 Unit cell: (115.648, 70.72, 82.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 801 8.00 N 776 7.00 C 2907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " 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 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 930.7 milliseconds 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1146 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 2 sheets defined 57.0% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 15 through 41 removed outlier: 4.283A pdb=" N VAL A 21 " --> pdb=" O GLN A 17 " (cutoff:3.500A) Proline residue: A 27 - end of helix removed outlier: 4.747A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASN A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 133 through 159 removed outlier: 3.687A pdb=" N GLN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 180 Processing helix chain 'A' and resid 185 through 213 removed outlier: 3.746A pdb=" N SER A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 243 removed outlier: 4.066A pdb=" N ARG A 219 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ALA A 220 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 267 Proline residue: A 257 - end of helix removed outlier: 4.009A pdb=" N ILE A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 299 through 302 No H-bonds generated for 'chain 'A' and resid 299 through 302' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 333 through 358 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.733A pdb=" N ASP A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 395 through 414 Processing helix chain 'A' and resid 421 through 448 Processing helix chain 'A' and resid 454 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 485 through 501 Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.757A pdb=" N LEU A 519 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS A 520 " --> pdb=" O GLN A 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.802A pdb=" N LEU B 18 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B 83 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS B 22 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 93 through 96 removed outlier: 3.566A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 669 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: 1.20 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 1 1.17 - 1.33: 1150 1.33 - 1.49: 1534 1.49 - 1.66: 1875 1.66 - 1.82: 53 Bond restraints: 4613 Sorted by residual: bond pdb=" CB PRO A 88 " pdb=" CG PRO A 88 " ideal model delta sigma weight residual 1.492 1.011 0.481 5.00e-02 4.00e+02 9.25e+01 bond pdb=" CG PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sigma weight residual 1.503 1.217 0.286 3.40e-02 8.65e+02 7.06e+01 bond pdb=" N PRO A 88 " pdb=" CA PRO A 88 " ideal model delta sigma weight residual 1.465 1.566 -0.101 2.03e-02 2.43e+03 2.49e+01 bond pdb=" CG PRO A 494 " pdb=" CD PRO A 494 " ideal model delta sigma weight residual 1.503 1.561 -0.058 3.40e-02 8.65e+02 2.91e+00 bond pdb=" CB PRO A 494 " pdb=" CG PRO A 494 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.60e+00 ... (remaining 4608 not shown) Histogram of bond angle deviations from ideal: 66.53 - 83.12: 2 83.12 - 99.70: 2 99.70 - 116.29: 3018 116.29 - 132.88: 3258 132.88 - 149.47: 12 Bond angle restraints: 6292 Sorted by residual: angle pdb=" CA PRO A 88 " pdb=" CB PRO A 88 " pdb=" CG PRO A 88 " ideal model delta sigma weight residual 104.50 66.53 37.97 1.90e+00 2.77e-01 3.99e+02 angle pdb=" N PRO A 88 " pdb=" CD PRO A 88 " pdb=" CG PRO A 88 " ideal model delta sigma weight residual 103.20 74.08 29.12 1.50e+00 4.44e-01 3.77e+02 angle pdb=" CB PRO A 88 " pdb=" CG PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sigma weight residual 106.10 149.47 -43.37 3.20e+00 9.77e-02 1.84e+02 angle pdb=" CA PRO A 88 " pdb=" N PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sigma weight residual 112.00 99.99 12.01 1.40e+00 5.10e-01 7.36e+01 angle pdb=" CA PRO A 494 " pdb=" N PRO A 494 " pdb=" CD PRO A 494 " ideal model delta sigma weight residual 112.00 102.70 9.30 1.40e+00 5.10e-01 4.41e+01 ... (remaining 6287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2316 17.69 - 35.37: 300 35.37 - 53.06: 73 53.06 - 70.75: 14 70.75 - 88.44: 10 Dihedral angle restraints: 2713 sinusoidal: 929 harmonic: 1784 Sorted by residual: dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sinusoidal sigma weight residual 93.00 27.55 65.45 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" N PRO A 88 " pdb=" CG PRO A 88 " pdb=" CD PRO A 88 " pdb=" CB PRO A 88 " ideal model delta sinusoidal sigma weight residual 30.00 107.54 -77.54 1 1.50e+01 4.44e-03 3.35e+01 dihedral pdb=" CA PRO A 88 " pdb=" CB PRO A 88 " pdb=" CG PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sinusoidal sigma weight residual 38.00 123.96 -85.96 1 2.00e+01 2.50e-03 2.23e+01 ... (remaining 2710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 564 0.048 - 0.095: 138 0.095 - 0.143: 31 0.143 - 0.190: 6 0.190 - 0.238: 3 Chirality restraints: 742 Sorted by residual: chirality pdb=" CA PRO A 494 " pdb=" N PRO A 494 " pdb=" C PRO A 494 " pdb=" CB PRO A 494 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA PRO A 88 " pdb=" N PRO A 88 " pdb=" C PRO A 88 " pdb=" CB PRO A 88 " both_signs ideal model delta sigma weight residual False 2.72 2.93 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO A 257 " pdb=" N PRO A 257 " pdb=" C PRO A 257 " pdb=" CB PRO A 257 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.11e-01 ... (remaining 739 not shown) Planarity restraints: 799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " 0.052 2.00e-02 2.50e+03 9.66e-02 9.34e+01 pdb=" C SER B 114 " -0.167 2.00e-02 2.50e+03 pdb=" O SER B 114 " 0.061 2.00e-02 2.50e+03 pdb=" N ALA B 115 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 493 " 0.070 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A 494 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 494 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 494 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 87 " 0.046 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO A 88 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.035 5.00e-02 4.00e+02 ... (remaining 796 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 170 2.71 - 3.25: 4879 3.25 - 3.80: 7758 3.80 - 4.35: 8556 4.35 - 4.90: 14406 Nonbonded interactions: 35769 Sorted by model distance: nonbonded pdb=" OG1 THR A 172 " pdb=" OG SER A 198 " model vdw 2.157 2.440 nonbonded pdb=" OD1 ASP A 70 " pdb=" N GLN A 74 " model vdw 2.257 2.520 nonbonded pdb=" OG SER A 401 " pdb=" O CYS A 433 " model vdw 2.267 2.440 nonbonded pdb=" NH1 ARG A 394 " pdb=" OG1 THR A 507 " model vdw 2.276 2.520 nonbonded pdb=" ND2 ASN A 39 " pdb=" O MET A 358 " model vdw 2.285 2.520 ... (remaining 35764 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 5.120 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 17.810 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 : 0.009 0.481 4613 Z= 0.380 Angle : 1.190 43.365 6292 Z= 0.569 Chirality : 0.046 0.238 742 Planarity : 0.007 0.100 799 Dihedral : 17.662 88.436 1561 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.23 % Allowed : 44.99 % Favored : 54.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.34), residues: 615 helix: 1.09 (0.27), residues: 357 sheet: 0.48 (0.82), residues: 48 loop : -1.34 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 109 HIS 0.002 0.001 HIS A 47 PHE 0.025 0.002 PHE A 262 TYR 0.016 0.001 TYR A 482 ARG 0.008 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 482 TYR cc_start: 0.7709 (t80) cc_final: 0.7377 (t80) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1090 time to fit residues: 14.3136 Evaluate side-chains 92 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 50.0000 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.0070 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.0480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4613 Z= 0.183 Angle : 0.713 13.191 6292 Z= 0.335 Chirality : 0.040 0.145 742 Planarity : 0.005 0.035 799 Dihedral : 4.844 59.585 671 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.03 % Allowed : 41.03 % Favored : 55.94 % 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: 0.43 (0.35), residues: 615 helix: 1.12 (0.28), residues: 357 sheet: 0.85 (0.83), residues: 47 loop : -1.27 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 109 HIS 0.001 0.000 HIS A 47 PHE 0.013 0.001 PHE A 347 TYR 0.016 0.001 TYR A 354 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8793 (tpt) cc_final: 0.8348 (tpt) REVERT: A 142 MET cc_start: 0.9610 (tpp) cc_final: 0.9278 (tpp) REVERT: A 482 TYR cc_start: 0.7579 (t80) cc_final: 0.7061 (t80) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 0.1033 time to fit residues: 15.8514 Evaluate side-chains 103 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 55 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 49 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4613 Z= 0.221 Angle : 0.658 9.645 6292 Z= 0.311 Chirality : 0.040 0.154 742 Planarity : 0.005 0.041 799 Dihedral : 4.633 57.083 671 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.20 % Allowed : 41.26 % Favored : 54.55 % 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: 0.44 (0.35), residues: 615 helix: 1.11 (0.28), residues: 357 sheet: 0.84 (0.83), residues: 48 loop : -1.24 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 109 HIS 0.002 0.001 HIS A 47 PHE 0.012 0.001 PHE A 262 TYR 0.013 0.001 TYR A 354 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8822 (tpt) cc_final: 0.8415 (tpt) REVERT: A 482 TYR cc_start: 0.7520 (t80) cc_final: 0.6962 (t80) outliers start: 18 outliers final: 17 residues processed: 106 average time/residue: 0.1171 time to fit residues: 17.2296 Evaluate side-chains 112 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 49 optimal weight: 0.0010 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4613 Z= 0.175 Angle : 0.658 10.529 6292 Z= 0.303 Chirality : 0.040 0.157 742 Planarity : 0.005 0.039 799 Dihedral : 4.498 56.563 671 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.83 % Allowed : 39.86 % Favored : 54.31 % 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: 0.42 (0.35), residues: 615 helix: 1.10 (0.28), residues: 357 sheet: 0.97 (0.84), residues: 47 loop : -1.29 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 86 HIS 0.001 0.000 HIS A 47 PHE 0.014 0.001 PHE A 347 TYR 0.008 0.001 TYR A 354 ARG 0.002 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9466 (pptt) cc_final: 0.9242 (pptt) REVERT: A 23 MET cc_start: 0.8795 (tpt) cc_final: 0.8404 (tpt) REVERT: A 482 TYR cc_start: 0.7531 (t80) cc_final: 0.6934 (t80) outliers start: 25 outliers final: 19 residues processed: 112 average time/residue: 0.1234 time to fit residues: 18.9249 Evaluate side-chains 113 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.0270 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 40.0000 chunk 40 optimal weight: 0.4980 chunk 30 optimal weight: 0.0060 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 overall best weight: 0.8856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4613 Z= 0.190 Angle : 0.672 10.743 6292 Z= 0.306 Chirality : 0.040 0.186 742 Planarity : 0.005 0.037 799 Dihedral : 4.398 55.239 671 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.06 % Allowed : 39.86 % Favored : 54.08 % 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 (0.35), residues: 615 helix: 1.03 (0.28), residues: 358 sheet: 0.95 (0.83), residues: 47 loop : -1.30 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 274 HIS 0.001 0.000 HIS A 47 PHE 0.012 0.001 PHE A 347 TYR 0.009 0.001 TYR A 354 ARG 0.002 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8803 (tpt) cc_final: 0.8422 (tpt) REVERT: A 161 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7496 (mmt90) REVERT: A 482 TYR cc_start: 0.7516 (t80) cc_final: 0.6875 (t80) outliers start: 26 outliers final: 22 residues processed: 117 average time/residue: 0.1346 time to fit residues: 21.2210 Evaluate side-chains 118 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4613 Z= 0.190 Angle : 0.704 11.177 6292 Z= 0.317 Chirality : 0.040 0.179 742 Planarity : 0.005 0.039 799 Dihedral : 4.293 53.607 671 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 7.23 % Allowed : 39.16 % Favored : 53.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.35), residues: 615 helix: 1.00 (0.28), residues: 358 sheet: 0.92 (0.81), residues: 51 loop : -1.30 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.001 0.000 HIS A 47 PHE 0.013 0.001 PHE A 347 TYR 0.009 0.001 TYR A 354 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 100 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 161 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7483 (mmt90) REVERT: A 234 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7639 (tm-30) REVERT: A 482 TYR cc_start: 0.7523 (t80) cc_final: 0.6988 (t80) outliers start: 31 outliers final: 23 residues processed: 123 average time/residue: 0.1208 time to fit residues: 20.3391 Evaluate side-chains 122 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 0.0020 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4613 Z= 0.214 Angle : 0.741 11.533 6292 Z= 0.331 Chirality : 0.040 0.162 742 Planarity : 0.005 0.035 799 Dihedral : 4.290 53.320 671 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.99 % Allowed : 39.39 % Favored : 53.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.35), residues: 615 helix: 0.98 (0.28), residues: 358 sheet: 1.09 (0.81), residues: 50 loop : -1.27 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 266 HIS 0.002 0.000 HIS A 47 PHE 0.015 0.001 PHE A 347 TYR 0.017 0.001 TYR A 354 ARG 0.001 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 99 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 482 TYR cc_start: 0.7596 (t80) cc_final: 0.6954 (t80) outliers start: 30 outliers final: 23 residues processed: 121 average time/residue: 0.1191 time to fit residues: 19.5992 Evaluate side-chains 117 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 46 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.0010 chunk 51 optimal weight: 50.0000 chunk 54 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4613 Z= 0.187 Angle : 0.773 12.023 6292 Z= 0.336 Chirality : 0.041 0.165 742 Planarity : 0.005 0.037 799 Dihedral : 4.230 52.665 671 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.36 % Allowed : 40.56 % Favored : 54.08 % 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: 0.31 (0.35), residues: 615 helix: 0.97 (0.28), residues: 358 sheet: 1.19 (0.83), residues: 50 loop : -1.37 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 86 HIS 0.001 0.000 HIS A 47 PHE 0.013 0.001 PHE A 347 TYR 0.008 0.001 TYR A 354 ARG 0.004 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.9553 (tpp) cc_final: 0.9238 (tpp) REVERT: A 367 MET cc_start: 0.8249 (mmt) cc_final: 0.8048 (mtt) REVERT: A 482 TYR cc_start: 0.7573 (t80) cc_final: 0.6934 (t80) outliers start: 23 outliers final: 20 residues processed: 111 average time/residue: 0.1134 time to fit residues: 17.5011 Evaluate side-chains 115 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.0470 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 40.0000 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 0.0670 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 30.0000 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4613 Z= 0.216 Angle : 0.795 11.970 6292 Z= 0.346 Chirality : 0.041 0.165 742 Planarity : 0.005 0.035 799 Dihedral : 4.106 46.351 671 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.53 % Allowed : 40.09 % Favored : 53.38 % 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: 0.29 (0.35), residues: 615 helix: 0.94 (0.28), residues: 357 sheet: 1.23 (0.84), residues: 50 loop : -1.34 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 109 HIS 0.001 0.000 HIS A 337 PHE 0.013 0.001 PHE A 347 TYR 0.008 0.001 TYR A 354 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 482 TYR cc_start: 0.7635 (t80) cc_final: 0.6955 (t80) outliers start: 28 outliers final: 26 residues processed: 118 average time/residue: 0.1097 time to fit residues: 17.9901 Evaluate side-chains 121 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 20.0000 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 50.0000 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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: 0.7851 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4613 Z= 0.238 Angle : 0.804 11.934 6292 Z= 0.353 Chirality : 0.043 0.245 742 Planarity : 0.005 0.035 799 Dihedral : 4.030 40.804 671 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 6.76 % Allowed : 40.09 % Favored : 53.15 % 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: 0.27 (0.35), residues: 615 helix: 0.92 (0.28), residues: 357 sheet: 1.26 (0.84), residues: 50 loop : -1.36 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 109 HIS 0.002 0.000 HIS A 47 PHE 0.013 0.001 PHE A 347 TYR 0.010 0.001 TYR A 444 ARG 0.002 0.000 ARG A 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.9594 (tpp) cc_final: 0.9363 (tpp) REVERT: A 482 TYR cc_start: 0.7595 (t80) cc_final: 0.6992 (t80) outliers start: 29 outliers final: 28 residues processed: 117 average time/residue: 0.1271 time to fit residues: 20.0383 Evaluate side-chains 123 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 518 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 0.0770 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.130251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.107493 restraints weight = 12614.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.110606 restraints weight = 6425.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.112701 restraints weight = 4136.086| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4613 Z= 0.202 Angle : 0.813 12.420 6292 Z= 0.353 Chirality : 0.042 0.208 742 Planarity : 0.005 0.036 799 Dihedral : 3.997 37.630 671 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 6.06 % Allowed : 41.26 % Favored : 52.68 % 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: 0.23 (0.35), residues: 615 helix: 0.90 (0.28), residues: 356 sheet: 1.23 (0.83), residues: 50 loop : -1.39 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 109 HIS 0.002 0.001 HIS A 47 PHE 0.013 0.001 PHE A 347 TYR 0.011 0.001 TYR A 444 ARG 0.008 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1296.16 seconds wall clock time: 24 minutes 7.06 seconds (1447.06 seconds total)