Starting phenix.real_space_refine on Tue Feb 11 20:35:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x8y_33060/02_2025/7x8y_33060_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x8y_33060/02_2025/7x8y_33060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x8y_33060/02_2025/7x8y_33060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x8y_33060/02_2025/7x8y_33060.map" model { file = "/net/cci-nas-00/data/ceres_data/7x8y_33060/02_2025/7x8y_33060_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x8y_33060/02_2025/7x8y_33060_trim.cif" } resolution = 4.1 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 2183 2.51 5 N 575 2.21 5 O 662 1.98 5 H 3296 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6731 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3222 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain: "H" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1865 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "L" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1630 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.63, per 1000 atoms: 0.54 Number of scatterers: 6731 At special positions: 0 Unit cell: (61.346, 72.952, 120.205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 O 662 8.00 N 575 7.00 C 2183 6.00 H 3296 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 642.7 milliseconds 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 802 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 6 sheets defined 9.8% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.482A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.637A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.166A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 61 through 62 removed outlier: 3.529A pdb=" N ARG H 50 " --> pdb=" O ASP H 61 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.530A pdb=" N SER L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR L 86 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) 87 hydrogen bonds defined for protein. 207 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 3296 1.04 - 1.24: 458 1.24 - 1.44: 1136 1.44 - 1.64: 1910 1.64 - 1.84: 18 Bond restraints: 6818 Sorted by residual: bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N GLN H 1 " pdb=" H GLN H 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" N ASP L 1 " pdb=" H ASP L 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 6813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 11371 1.03 - 2.06: 794 2.06 - 3.08: 44 3.08 - 4.11: 17 4.11 - 5.14: 3 Bond angle restraints: 12229 Sorted by residual: angle pdb=" N GLY H 26 " pdb=" CA GLY H 26 " pdb=" C GLY H 26 " ideal model delta sigma weight residual 114.16 119.30 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" N GLY H 57 " pdb=" CA GLY H 57 " pdb=" C GLY H 57 " ideal model delta sigma weight residual 114.48 111.74 2.74 1.19e+00 7.06e-01 5.31e+00 angle pdb=" CB ARG A 346 " pdb=" CG ARG A 346 " pdb=" CD ARG A 346 " ideal model delta sigma weight residual 111.30 115.18 -3.88 2.30e+00 1.89e-01 2.84e+00 angle pdb=" CG ARG A 346 " pdb=" CD ARG A 346 " pdb=" NE ARG A 346 " ideal model delta sigma weight residual 112.00 115.56 -3.56 2.20e+00 2.07e-01 2.62e+00 angle pdb=" CA GLN H 1 " pdb=" N GLN H 1 " pdb=" H GLN H 1 " ideal model delta sigma weight residual 114.00 109.44 4.56 3.00e+00 1.11e-01 2.31e+00 ... (remaining 12224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 2917 16.28 - 32.56: 282 32.56 - 48.83: 74 48.83 - 65.11: 25 65.11 - 81.39: 7 Dihedral angle restraints: 3305 sinusoidal: 1760 harmonic: 1545 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 20.07 72.93 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CA GLY H 26 " pdb=" C GLY H 26 " pdb=" N PHE H 27 " pdb=" CA PHE H 27 " ideal model delta harmonic sigma weight residual 180.00 157.37 22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA SER H 25 " pdb=" C SER H 25 " pdb=" N GLY H 26 " pdb=" CA GLY H 26 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 3302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 292 0.027 - 0.053: 156 0.053 - 0.080: 35 0.080 - 0.107: 26 0.107 - 0.133: 12 Chirality restraints: 521 Sorted by residual: chirality pdb=" CA VAL H 2 " pdb=" N VAL H 2 " pdb=" C VAL H 2 " pdb=" CB VAL H 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA VAL A 362 " pdb=" N VAL A 362 " pdb=" C VAL A 362 " pdb=" CB VAL A 362 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA VAL L 58 " pdb=" N VAL L 58 " pdb=" C VAL L 58 " pdb=" CB VAL L 58 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 518 not shown) Planarity restraints: 1031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 408 " 0.096 9.50e-02 1.11e+02 3.22e-02 1.24e+00 pdb=" NE ARG A 408 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 408 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 408 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 408 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 408 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 408 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 408 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 408 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 346 " -0.079 9.50e-02 1.11e+02 2.68e-02 1.15e+00 pdb=" NE ARG A 346 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 346 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 346 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 346 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 346 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 346 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 346 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 346 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 112 " 0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO H 113 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO H 113 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO H 113 " 0.014 5.00e-02 4.00e+02 ... (remaining 1028 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 610 2.21 - 2.81: 13812 2.81 - 3.41: 16511 3.41 - 4.00: 21961 4.00 - 4.60: 32493 Nonbonded interactions: 85387 Sorted by model distance: nonbonded pdb=" H LYS A 462 " pdb=" OE2 GLU A 465 " model vdw 1.617 2.450 nonbonded pdb=" OE1 GLN L 55 " pdb=" H GLY L 56 " model vdw 1.631 2.450 nonbonded pdb=" HZ2 LYS A 444 " pdb=" O GLY A 447 " model vdw 1.648 2.450 nonbonded pdb=" O SER H 112 " pdb=" HE1 TRP H 115 " model vdw 1.678 2.450 nonbonded pdb=" OD1 ASN A 422 " pdb=" H ARG A 454 " model vdw 1.694 2.450 ... (remaining 85382 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.140 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: 0.130 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.500 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 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 : 0.003 0.033 3522 Z= 0.174 Angle : 0.529 5.138 4787 Z= 0.283 Chirality : 0.040 0.133 521 Planarity : 0.004 0.042 615 Dihedral : 14.084 81.388 1267 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.09 (0.38), residues: 434 helix: -4.37 (0.55), residues: 26 sheet: -1.42 (0.44), residues: 133 loop : -2.23 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.016 0.001 PHE L 71 TYR 0.013 0.001 TYR L 36 ARG 0.010 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 LEU cc_start: 0.8460 (pt) cc_final: 0.8244 (pt) REVERT: H 56 ASP cc_start: 0.5517 (t0) cc_final: 0.5221 (t0) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.5484 time to fit residues: 48.0228 Evaluate side-chains 42 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.0270 chunk 32 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.052356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.040853 restraints weight = 76243.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.042863 restraints weight = 32517.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.044209 restraints weight = 18024.004| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3522 Z= 0.192 Angle : 0.520 4.887 4787 Z= 0.280 Chirality : 0.039 0.139 521 Planarity : 0.004 0.038 615 Dihedral : 5.077 42.404 504 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % 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: -2.91 (0.37), residues: 434 helix: -4.24 (0.48), residues: 32 sheet: -0.97 (0.48), residues: 117 loop : -2.19 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.016 0.001 PHE L 71 TYR 0.006 0.001 TYR L 36 ARG 0.004 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LYS cc_start: 0.9675 (mppt) cc_final: 0.9344 (mmtt) REVERT: H 46 GLU cc_start: 0.9077 (mp0) cc_final: 0.8721 (mp0) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.4757 time to fit residues: 28.8260 Evaluate side-chains 33 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 38 optimal weight: 30.0000 chunk 4 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.050457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.039019 restraints weight = 76377.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.041008 restraints weight = 32435.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.042319 restraints weight = 17851.891| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3522 Z= 0.257 Angle : 0.539 4.906 4787 Z= 0.292 Chirality : 0.040 0.138 521 Planarity : 0.004 0.033 615 Dihedral : 4.875 31.611 504 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % 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: -2.93 (0.38), residues: 434 helix: -4.27 (0.49), residues: 33 sheet: -1.08 (0.47), residues: 123 loop : -2.15 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.025 0.002 PHE A 392 TYR 0.013 0.001 TYR A 508 ARG 0.003 0.001 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LYS cc_start: 0.9682 (mppt) cc_final: 0.9411 (mmtm) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.5278 time to fit residues: 26.2955 Evaluate side-chains 29 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN H 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.049341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.037853 restraints weight = 76086.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.039820 restraints weight = 32579.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.041174 restraints weight = 17904.288| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3522 Z= 0.232 Angle : 0.523 4.718 4787 Z= 0.281 Chirality : 0.039 0.136 521 Planarity : 0.004 0.038 615 Dihedral : 4.526 22.127 504 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.27 % Allowed : 1.87 % Favored : 97.86 % 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: -2.70 (0.38), residues: 434 helix: -3.69 (0.67), residues: 31 sheet: -1.18 (0.47), residues: 120 loop : -1.93 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 35 HIS 0.002 0.001 HIS A 519 PHE 0.014 0.002 PHE L 71 TYR 0.009 0.001 TYR L 36 ARG 0.002 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LYS cc_start: 0.9674 (mppt) cc_final: 0.9416 (mmtm) REVERT: L 97 THR cc_start: 0.8350 (m) cc_final: 0.7722 (m) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.4547 time to fit residues: 24.7416 Evaluate side-chains 29 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.048963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.037938 restraints weight = 78214.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.039888 restraints weight = 32893.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.041180 restraints weight = 17914.978| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3522 Z= 0.209 Angle : 0.502 4.471 4787 Z= 0.270 Chirality : 0.040 0.132 521 Planarity : 0.004 0.034 615 Dihedral : 4.436 21.771 504 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.39), residues: 434 helix: -2.84 (1.01), residues: 25 sheet: -1.29 (0.46), residues: 119 loop : -1.90 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.013 0.001 PHE L 71 TYR 0.011 0.001 TYR A 508 ARG 0.002 0.000 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LYS cc_start: 0.9685 (mppt) cc_final: 0.9421 (mmtm) REVERT: H 56 ASP cc_start: 0.8774 (t0) cc_final: 0.8494 (t0) REVERT: L 97 THR cc_start: 0.8387 (m) cc_final: 0.7762 (m) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.4979 time to fit residues: 24.9510 Evaluate side-chains 29 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.049140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.038032 restraints weight = 77980.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.039962 restraints weight = 33245.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.041242 restraints weight = 18271.347| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3522 Z= 0.213 Angle : 0.518 4.369 4787 Z= 0.277 Chirality : 0.039 0.133 521 Planarity : 0.004 0.059 615 Dihedral : 4.448 22.091 504 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % 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: -2.53 (0.39), residues: 434 helix: -3.01 (0.94), residues: 25 sheet: -1.20 (0.47), residues: 118 loop : -1.85 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 35 HIS 0.002 0.001 HIS A 519 PHE 0.012 0.001 PHE A 392 TYR 0.011 0.001 TYR A 508 ARG 0.007 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LYS cc_start: 0.9664 (mppt) cc_final: 0.9396 (mmtm) REVERT: H 56 ASP cc_start: 0.8876 (t0) cc_final: 0.8644 (t70) REVERT: L 97 THR cc_start: 0.8408 (m) cc_final: 0.7859 (m) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.4675 time to fit residues: 23.9990 Evaluate side-chains 31 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 30.0000 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 30.0000 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.048733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.038002 restraints weight = 77428.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.039868 restraints weight = 32725.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.041153 restraints weight = 17992.652| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3522 Z= 0.257 Angle : 0.541 4.514 4787 Z= 0.293 Chirality : 0.039 0.147 521 Planarity : 0.004 0.041 615 Dihedral : 4.758 22.723 504 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: -2.45 (0.40), residues: 434 helix: -2.50 (1.19), residues: 19 sheet: -1.10 (0.48), residues: 118 loop : -1.89 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.011 0.002 PHE L 71 TYR 0.011 0.001 TYR A 508 ARG 0.009 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.9670 (mt) cc_final: 0.9388 (tp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.5036 time to fit residues: 24.6391 Evaluate side-chains 28 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.048759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.037848 restraints weight = 79863.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.039782 restraints weight = 34186.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.041090 restraints weight = 18693.732| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3522 Z= 0.204 Angle : 0.512 4.128 4787 Z= 0.275 Chirality : 0.039 0.134 521 Planarity : 0.004 0.040 615 Dihedral : 4.659 22.930 504 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -2.44 (0.40), residues: 434 helix: -2.59 (0.94), residues: 25 sheet: -1.07 (0.48), residues: 121 loop : -1.86 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 353 HIS 0.001 0.001 HIS A 519 PHE 0.009 0.001 PHE A 392 TYR 0.017 0.001 TYR A 508 ARG 0.006 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.9410 (m-10) cc_final: 0.9197 (m-10) REVERT: A 434 ILE cc_start: 0.9646 (mt) cc_final: 0.9355 (tp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.6045 time to fit residues: 29.0027 Evaluate side-chains 32 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 3 optimal weight: 0.0270 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 overall best weight: 3.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.049121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.038103 restraints weight = 79031.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.040100 restraints weight = 33751.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.041427 restraints weight = 18415.540| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3522 Z= 0.169 Angle : 0.489 4.075 4787 Z= 0.261 Chirality : 0.039 0.136 521 Planarity : 0.005 0.067 615 Dihedral : 4.381 21.657 504 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.34 (0.40), residues: 434 helix: -2.49 (0.96), residues: 25 sheet: -0.99 (0.49), residues: 121 loop : -1.79 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.001 0.001 HIS A 519 PHE 0.010 0.001 PHE A 392 TYR 0.013 0.001 TYR A 508 ARG 0.006 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.9641 (mt) cc_final: 0.9339 (tp) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.5492 time to fit residues: 28.0448 Evaluate side-chains 29 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.048637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.037466 restraints weight = 80165.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.039429 restraints weight = 33971.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.040722 restraints weight = 18479.721| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3522 Z= 0.194 Angle : 0.498 4.016 4787 Z= 0.267 Chirality : 0.039 0.134 521 Planarity : 0.004 0.034 615 Dihedral : 4.430 22.018 504 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -2.24 (0.40), residues: 434 helix: -2.41 (0.99), residues: 25 sheet: -0.96 (0.48), residues: 129 loop : -1.72 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.009 0.001 PHE L 71 TYR 0.016 0.001 TYR A 508 ARG 0.006 0.001 ARG A 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.9360 (m-10) cc_final: 0.9131 (m-10) REVERT: A 434 ILE cc_start: 0.9649 (mt) cc_final: 0.9344 (tp) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.5292 time to fit residues: 24.9966 Evaluate side-chains 32 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 32 optimal weight: 0.4980 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.049047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.037804 restraints weight = 78497.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.039784 restraints weight = 33368.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.041106 restraints weight = 18150.222| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3522 Z= 0.150 Angle : 0.484 3.901 4787 Z= 0.258 Chirality : 0.040 0.135 521 Planarity : 0.004 0.036 615 Dihedral : 4.270 21.140 504 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -2.15 (0.40), residues: 434 helix: -2.08 (1.08), residues: 25 sheet: -1.01 (0.48), residues: 125 loop : -1.62 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.010 0.001 PHE A 392 TYR 0.015 0.001 TYR A 508 ARG 0.005 0.000 ARG A 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2645.37 seconds wall clock time: 47 minutes 29.41 seconds (2849.41 seconds total)