Starting phenix.real_space_refine on Fri Aug 2 17:29:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3s_42952/08_2024/8v3s_42952.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3s_42952/08_2024/8v3s_42952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3s_42952/08_2024/8v3s_42952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3s_42952/08_2024/8v3s_42952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3s_42952/08_2024/8v3s_42952.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3s_42952/08_2024/8v3s_42952.cif" } resolution = 3.6 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= 0.001 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 Zn 1 6.06 5 S 21 5.16 5 C 2492 2.51 5 N 697 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 4": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 549": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A ARG 598": "NH1" <-> "NH2" Residue "M GLU 1001": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3909 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3870 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 35, 'TRANS': 463} Chain breaks: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 122 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 4.36, per 1000 atoms: 1.12 Number of scatterers: 3909 At special positions: 0 Unit cell: (80.925, 73.455, 69.72, 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) Zn 1 29.99 S 21 16.00 O 698 8.00 N 697 7.00 C 2492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 653.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" ND1 HIS A 434 " pdb="ZN ZN A 701 " - pdb=" ND1 HIS A 252 " 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 948 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 5 sheets defined 31.5% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 256 through 270 removed outlier: 3.865A pdb=" N PHE A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 323 through 340 Processing helix chain 'A' and resid 451 through 467 removed outlier: 4.362A pdb=" N TYR A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Proline residue: A 462 - end of helix Processing helix chain 'A' and resid 481 through 486 removed outlier: 3.844A pdb=" N TYR A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 removed outlier: 3.659A pdb=" N GLY A 497 " --> pdb=" O SER A 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 494 through 497' Processing helix chain 'A' and resid 498 through 508 Processing helix chain 'A' and resid 551 through 570 removed outlier: 3.976A pdb=" N ALA A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 585 through 601 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 5.232A pdb=" N THR A 112 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ARG A 118 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 removed outlier: 6.733A pdb=" N TYR A 52 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASN A 91 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE A 54 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 128 Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 198 removed outlier: 7.153A pdb=" N VAL A 205 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 245 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE A 289 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 247 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A 244 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL A 431 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE A 246 " --> pdb=" O VAL A 431 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LEU A 433 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER A 248 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N GLY A 435 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 220 removed outlier: 5.843A pdb=" N ASP A 219 " --> pdb=" O ARG A 238 " (cutoff:3.500A) 145 hydrogen bonds defined for protein. 408 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: 1.03 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 713 1.31 - 1.44: 1089 1.44 - 1.57: 2182 1.57 - 1.69: 4 1.69 - 1.82: 31 Bond restraints: 4019 Sorted by residual: bond pdb=" N GLU M1001 " pdb=" CA GLU M1001 " ideal model delta sigma weight residual 1.458 1.525 -0.067 1.90e-02 2.77e+03 1.23e+01 bond pdb=" CZ ARG A 276 " pdb=" NH2 ARG A 276 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.10e+00 bond pdb=" CA GLU M1001 " pdb=" C GLU M1001 " ideal model delta sigma weight residual 1.525 1.588 -0.063 2.10e-02 2.27e+03 9.04e+00 bond pdb=" CZ ARG A 250 " pdb=" NH2 ARG A 250 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 8.96e+00 bond pdb=" CZ ARG A 238 " pdb=" NH2 ARG A 238 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.40e+00 ... (remaining 4014 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.15: 102 105.15 - 112.49: 1841 112.49 - 119.84: 1502 119.84 - 127.18: 1980 127.18 - 134.52: 39 Bond angle restraints: 5464 Sorted by residual: angle pdb=" N ILE A 578 " pdb=" CA ILE A 578 " pdb=" C ILE A 578 " ideal model delta sigma weight residual 110.62 116.35 -5.73 1.02e+00 9.61e-01 3.16e+01 angle pdb=" C SER A 539 " pdb=" N PRO A 540 " pdb=" CA PRO A 540 " ideal model delta sigma weight residual 119.66 115.66 4.00 7.20e-01 1.93e+00 3.09e+01 angle pdb=" C ALA A 545 " pdb=" CA ALA A 545 " pdb=" CB ALA A 545 " ideal model delta sigma weight residual 116.54 110.26 6.28 1.15e+00 7.56e-01 2.98e+01 angle pdb=" C SER A 548 " pdb=" CA SER A 548 " pdb=" CB SER A 548 " ideal model delta sigma weight residual 117.23 110.47 6.76 1.36e+00 5.41e-01 2.47e+01 angle pdb=" OE1 GLN A 475 " pdb=" CD GLN A 475 " pdb=" NE2 GLN A 475 " ideal model delta sigma weight residual 122.60 117.71 4.89 1.00e+00 1.00e+00 2.39e+01 ... (remaining 5459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2194 17.82 - 35.65: 145 35.65 - 53.47: 25 53.47 - 71.30: 5 71.30 - 89.12: 3 Dihedral angle restraints: 2372 sinusoidal: 904 harmonic: 1468 Sorted by residual: dihedral pdb=" CA TYR A 519 " pdb=" C TYR A 519 " pdb=" N ASN A 520 " pdb=" CA ASN A 520 " ideal model delta harmonic sigma weight residual -180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA HIS A 583 " pdb=" C HIS A 583 " pdb=" N SER A 584 " pdb=" CA SER A 584 " ideal model delta harmonic sigma weight residual 180.00 -161.31 -18.69 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ARG A 72 " pdb=" C ARG A 72 " pdb=" N SER A 73 " pdb=" CA SER A 73 " ideal model delta harmonic sigma weight residual -180.00 -161.51 -18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 375 0.067 - 0.133: 130 0.133 - 0.200: 60 0.200 - 0.266: 14 0.266 - 0.333: 6 Chirality restraints: 585 Sorted by residual: chirality pdb=" CA SER A 16 " pdb=" N SER A 16 " pdb=" C SER A 16 " pdb=" CB SER A 16 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA GLU M1001 " pdb=" N GLU M1001 " pdb=" C GLU M1001 " pdb=" CB GLU M1001 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA GLU M 3 " pdb=" N GLU M 3 " pdb=" C GLU M 3 " pdb=" CB GLU M 3 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 582 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 519 " 0.050 2.00e-02 2.50e+03 2.65e-02 1.40e+01 pdb=" CG TYR A 519 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 519 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 519 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 519 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 519 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 519 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 519 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 192 " 0.037 2.00e-02 2.50e+03 2.90e-02 1.26e+01 pdb=" CG HIS A 192 " -0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS A 192 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS A 192 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 192 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 192 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 335 " -0.039 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" CG TYR A 335 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR A 335 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 335 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 335 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A 335 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 335 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 335 " -0.046 2.00e-02 2.50e+03 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 2 2.09 - 2.79: 644 2.79 - 3.49: 5583 3.49 - 4.20: 9666 4.20 - 4.90: 16701 Nonbonded interactions: 32596 Sorted by model distance: nonbonded pdb=" CD GLU M 3 " pdb=" N GLU M1001 " model vdw 1.385 3.350 nonbonded pdb=" OE1 GLU A 255 " pdb="ZN ZN A 701 " model vdw 1.978 2.230 nonbonded pdb=" OE2 GLU A 255 " pdb="ZN ZN A 701 " model vdw 2.097 2.230 nonbonded pdb=" CD GLU A 255 " pdb="ZN ZN A 701 " model vdw 2.263 2.460 nonbonded pdb=" OE1 GLU M 3 " pdb=" N GLU M1001 " model vdw 2.294 3.120 ... (remaining 32591 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: 7.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.410 Find NCS groups from input model: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.011 0.067 4019 Z= 0.750 Angle : 1.522 7.475 5464 Z= 1.003 Chirality : 0.086 0.333 585 Planarity : 0.011 0.067 718 Dihedral : 12.860 89.124 1424 Min Nonbonded Distance : 1.385 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.33), residues: 491 helix: -0.47 (0.35), residues: 143 sheet: -0.15 (0.58), residues: 72 loop : -1.05 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.008 TRP A 575 HIS 0.018 0.006 HIS A 436 PHE 0.036 0.006 PHE A 265 TYR 0.050 0.012 TYR A 519 ARG 0.016 0.002 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 3 LEU cc_start: 0.8260 (mt) cc_final: 0.8056 (mm) REVERT: A 52 TYR cc_start: 0.7967 (m-80) cc_final: 0.7673 (m-10) REVERT: A 69 ASN cc_start: 0.7676 (t0) cc_final: 0.7414 (t0) REVERT: A 307 ARG cc_start: 0.7254 (ttp80) cc_final: 0.6802 (ttp-170) REVERT: A 521 THR cc_start: 0.8097 (t) cc_final: 0.7822 (m) REVERT: A 557 GLN cc_start: 0.7552 (tp-100) cc_final: 0.6999 (tp-100) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1870 time to fit residues: 16.1160 Evaluate side-chains 38 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.1980 chunk 37 optimal weight: 0.0770 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 23 optimal weight: 0.0770 chunk 28 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 overall best weight: 0.0894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4019 Z= 0.170 Angle : 0.606 12.632 5464 Z= 0.303 Chirality : 0.042 0.145 585 Planarity : 0.005 0.043 718 Dihedral : 5.414 72.678 557 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.74 % Allowed : 11.41 % Favored : 86.85 % 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: -0.16 (0.36), residues: 491 helix: 0.86 (0.40), residues: 143 sheet: 0.09 (0.57), residues: 74 loop : -0.66 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 119 HIS 0.004 0.001 HIS A 596 PHE 0.016 0.001 PHE A 153 TYR 0.018 0.002 TYR A 461 ARG 0.006 0.001 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.463 Fit side-chains REVERT: A 69 ASN cc_start: 0.7965 (t0) cc_final: 0.7698 (t0) REVERT: A 549 ARG cc_start: 0.7608 (mmt180) cc_final: 0.7283 (mpt90) REVERT: A 586 LEU cc_start: 0.7419 (tp) cc_final: 0.7139 (tp) outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.1917 time to fit residues: 12.4609 Evaluate side-chains 41 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 578 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.0470 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.0470 chunk 35 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4019 Z= 0.317 Angle : 0.642 10.555 5464 Z= 0.328 Chirality : 0.045 0.168 585 Planarity : 0.005 0.045 718 Dihedral : 5.745 81.838 557 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.23 % Allowed : 12.66 % Favored : 84.12 % 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: -0.12 (0.36), residues: 491 helix: 0.91 (0.41), residues: 143 sheet: 0.07 (0.55), residues: 77 loop : -0.63 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 119 HIS 0.003 0.001 HIS A 511 PHE 0.013 0.002 PHE A 268 TYR 0.027 0.002 TYR A 161 ARG 0.015 0.001 ARG A 598 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.471 Fit side-chains REVERT: A 69 ASN cc_start: 0.8210 (t0) cc_final: 0.7736 (t0) REVERT: A 150 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8276 (p) REVERT: A 595 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7363 (mtmm) outliers start: 13 outliers final: 9 residues processed: 51 average time/residue: 0.1518 time to fit residues: 10.1625 Evaluate side-chains 42 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 578 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 47 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 39 optimal weight: 0.1980 chunk 26 optimal weight: 0.0870 chunk 0 optimal weight: 0.9990 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4019 Z= 0.239 Angle : 0.571 10.701 5464 Z= 0.288 Chirality : 0.042 0.132 585 Planarity : 0.005 0.045 718 Dihedral : 5.549 82.934 557 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.97 % Allowed : 14.64 % Favored : 81.39 % 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: -0.06 (0.36), residues: 491 helix: 1.00 (0.41), residues: 143 sheet: 0.49 (0.54), residues: 85 loop : -0.80 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 57 HIS 0.003 0.001 HIS A 336 PHE 0.013 0.001 PHE A 286 TYR 0.019 0.002 TYR A 161 ARG 0.005 0.000 ARG A 598 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 38 time to evaluate : 0.443 Fit side-chains REVERT: A 69 ASN cc_start: 0.8219 (t0) cc_final: 0.7705 (t0) REVERT: A 135 PHE cc_start: 0.7561 (t80) cc_final: 0.7221 (t80) REVERT: A 150 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8218 (p) REVERT: A 191 TYR cc_start: 0.8170 (t80) cc_final: 0.7800 (t80) REVERT: A 314 GLN cc_start: 0.7401 (mm-40) cc_final: 0.7186 (mm-40) outliers start: 16 outliers final: 12 residues processed: 52 average time/residue: 0.1371 time to fit residues: 9.4926 Evaluate side-chains 47 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 34 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 578 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 42 optimal weight: 0.0770 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4019 Z= 0.285 Angle : 0.596 9.972 5464 Z= 0.300 Chirality : 0.042 0.132 585 Planarity : 0.005 0.046 718 Dihedral : 5.621 84.703 557 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.23 % Allowed : 15.14 % Favored : 81.64 % 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: -0.12 (0.36), residues: 491 helix: 0.93 (0.41), residues: 140 sheet: 0.45 (0.54), residues: 90 loop : -0.82 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 119 HIS 0.003 0.001 HIS A 192 PHE 0.015 0.002 PHE A 286 TYR 0.018 0.002 TYR A 161 ARG 0.003 0.001 ARG A 598 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 37 time to evaluate : 0.444 Fit side-chains REVERT: A 69 ASN cc_start: 0.8289 (t0) cc_final: 0.7948 (t0) REVERT: A 135 PHE cc_start: 0.7798 (t80) cc_final: 0.7317 (t80) REVERT: A 459 MET cc_start: 0.8641 (mtt) cc_final: 0.8304 (mtt) REVERT: A 595 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7399 (mtmm) outliers start: 13 outliers final: 13 residues processed: 49 average time/residue: 0.1339 time to fit residues: 8.8020 Evaluate side-chains 46 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 33 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 578 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.3980 chunk 47 optimal weight: 0.1980 chunk 39 optimal weight: 0.4980 chunk 21 optimal weight: 0.3980 chunk 3 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 45 optimal weight: 0.0770 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 0.0870 chunk 34 optimal weight: 0.0980 overall best weight: 0.0892 ------------------------------------------------------------------------------- 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: 0.7463 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4019 Z= 0.155 Angle : 0.548 9.331 5464 Z= 0.271 Chirality : 0.040 0.130 585 Planarity : 0.004 0.048 718 Dihedral : 5.426 84.828 557 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.83 % Favored : 97.96 % Rotamer: Outliers : 2.48 % Allowed : 15.88 % Favored : 81.64 % 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: 0.12 (0.36), residues: 491 helix: 1.14 (0.41), residues: 144 sheet: 0.78 (0.56), residues: 85 loop : -0.75 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 57 HIS 0.003 0.001 HIS A 336 PHE 0.009 0.001 PHE A 54 TYR 0.018 0.001 TYR A 161 ARG 0.003 0.000 ARG A 598 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.459 Fit side-chains REVERT: A 69 ASN cc_start: 0.8217 (t0) cc_final: 0.7643 (t0) REVERT: A 135 PHE cc_start: 0.7695 (t80) cc_final: 0.7265 (t80) REVERT: A 136 VAL cc_start: 0.8692 (t) cc_final: 0.8483 (p) REVERT: A 459 MET cc_start: 0.8690 (mtt) cc_final: 0.8396 (mtt) REVERT: A 595 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7424 (mtmm) outliers start: 10 outliers final: 10 residues processed: 45 average time/residue: 0.1427 time to fit residues: 8.5300 Evaluate side-chains 45 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 583 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.0670 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 0.0670 chunk 29 optimal weight: 0.0060 chunk 28 optimal weight: 0.0670 chunk 21 optimal weight: 0.1980 chunk 18 optimal weight: 0.0980 chunk 14 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.0270 chunk 32 optimal weight: 0.6980 overall best weight: 0.0468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4019 Z= 0.136 Angle : 0.526 8.535 5464 Z= 0.258 Chirality : 0.039 0.131 585 Planarity : 0.004 0.049 718 Dihedral : 5.291 85.283 557 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.24 % Favored : 97.56 % Rotamer: Outliers : 2.48 % Allowed : 15.14 % Favored : 82.38 % 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: 0.33 (0.37), residues: 491 helix: 1.42 (0.42), residues: 146 sheet: 0.94 (0.57), residues: 85 loop : -0.73 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 119 HIS 0.003 0.001 HIS A 336 PHE 0.007 0.001 PHE A 109 TYR 0.016 0.001 TYR A 161 ARG 0.003 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.449 Fit side-chains REVERT: A 69 ASN cc_start: 0.8214 (t0) cc_final: 0.7620 (t0) REVERT: A 430 TYR cc_start: 0.8498 (t80) cc_final: 0.7983 (t80) REVERT: A 440 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7758 (mtm180) REVERT: A 459 MET cc_start: 0.8711 (mtt) cc_final: 0.8401 (mtt) REVERT: A 595 LYS cc_start: 0.8150 (mtpp) cc_final: 0.7482 (mtmm) outliers start: 10 outliers final: 9 residues processed: 50 average time/residue: 0.1568 time to fit residues: 10.1862 Evaluate side-chains 48 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 583 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 45 optimal weight: 0.0980 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 26 optimal weight: 0.0970 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 13 optimal weight: 0.2980 overall best weight: 0.1978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4019 Z= 0.216 Angle : 0.560 8.187 5464 Z= 0.278 Chirality : 0.041 0.127 585 Planarity : 0.004 0.048 718 Dihedral : 5.405 86.854 557 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.44 % Favored : 97.35 % Rotamer: Outliers : 3.72 % Allowed : 15.14 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.37), residues: 491 helix: 1.51 (0.42), residues: 140 sheet: 1.00 (0.57), residues: 85 loop : -0.77 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 119 HIS 0.003 0.001 HIS A 336 PHE 0.031 0.002 PHE A 135 TYR 0.015 0.001 TYR A 161 ARG 0.002 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 0.410 Fit side-chains REVERT: A 69 ASN cc_start: 0.8179 (t0) cc_final: 0.7581 (t0) REVERT: A 440 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7602 (mtm180) REVERT: A 459 MET cc_start: 0.8706 (mtt) cc_final: 0.8416 (mtt) REVERT: A 595 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7483 (mtmm) outliers start: 15 outliers final: 11 residues processed: 50 average time/residue: 0.1499 time to fit residues: 9.7341 Evaluate side-chains 48 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 583 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 43 optimal weight: 0.0170 chunk 28 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.0060 chunk 48 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4019 Z= 0.339 Angle : 0.626 8.124 5464 Z= 0.315 Chirality : 0.043 0.139 585 Planarity : 0.005 0.047 718 Dihedral : 5.706 88.579 557 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.46 % Favored : 96.33 % Rotamer: Outliers : 4.22 % Allowed : 13.65 % Favored : 82.13 % 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: 0.04 (0.37), residues: 491 helix: 1.08 (0.41), residues: 140 sheet: 0.70 (0.55), residues: 95 loop : -0.82 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 119 HIS 0.004 0.001 HIS A 336 PHE 0.035 0.002 PHE A 135 TYR 0.015 0.002 TYR A 161 ARG 0.005 0.001 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 37 time to evaluate : 0.402 Fit side-chains REVERT: A 69 ASN cc_start: 0.8244 (t0) cc_final: 0.8038 (t0) REVERT: A 291 MET cc_start: 0.8704 (mtt) cc_final: 0.8436 (mtm) REVERT: A 440 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7688 (mtm180) REVERT: A 459 MET cc_start: 0.8657 (mtt) cc_final: 0.8386 (mtt) REVERT: A 595 LYS cc_start: 0.8187 (mtpp) cc_final: 0.7756 (mtmm) outliers start: 17 outliers final: 16 residues processed: 50 average time/residue: 0.1682 time to fit residues: 10.6049 Evaluate side-chains 50 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 33 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 583 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.0770 chunk 23 optimal weight: 0.0670 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 35 optimal weight: 0.0980 chunk 5 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 39 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 overall best weight: 0.1676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4019 Z= 0.200 Angle : 0.571 8.048 5464 Z= 0.285 Chirality : 0.041 0.140 585 Planarity : 0.004 0.049 718 Dihedral : 5.532 88.194 557 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.44 % Favored : 97.35 % Rotamer: Outliers : 3.47 % Allowed : 14.14 % Favored : 82.38 % 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: 0.25 (0.37), residues: 491 helix: 1.35 (0.41), residues: 138 sheet: 0.98 (0.57), residues: 85 loop : -0.74 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 119 HIS 0.003 0.001 HIS A 336 PHE 0.024 0.001 PHE A 135 TYR 0.016 0.001 TYR A 161 ARG 0.008 0.001 ARG A 537 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.440 Fit side-chains REVERT: A 69 ASN cc_start: 0.8160 (t0) cc_final: 0.7750 (t0) REVERT: A 150 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8161 (p) REVERT: A 440 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7756 (mtm180) REVERT: A 459 MET cc_start: 0.8687 (mtt) cc_final: 0.8372 (mtt) REVERT: A 595 LYS cc_start: 0.8220 (mtpp) cc_final: 0.7808 (mtmm) outliers start: 14 outliers final: 12 residues processed: 52 average time/residue: 0.1470 time to fit residues: 10.0982 Evaluate side-chains 50 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 36 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 583 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.3980 chunk 34 optimal weight: 0.0970 chunk 2 optimal weight: 0.0570 chunk 28 optimal weight: 0.0970 chunk 44 optimal weight: 0.0170 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 0.3980 chunk 1 optimal weight: 0.0870 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 chunk 19 optimal weight: 0.0370 overall best weight: 0.0550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 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 = 0.3399 r_free = 0.3399 target = 0.112032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.098490 restraints weight = 6217.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.101362 restraints weight = 3660.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103209 restraints weight = 2520.639| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4019 Z= 0.147 Angle : 0.544 8.052 5464 Z= 0.269 Chirality : 0.040 0.136 585 Planarity : 0.004 0.050 718 Dihedral : 5.402 88.829 557 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.44 % Favored : 97.35 % Rotamer: Outliers : 2.48 % Allowed : 15.63 % Favored : 81.89 % 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 (0.37), residues: 491 helix: 1.52 (0.42), residues: 138 sheet: 1.13 (0.58), residues: 85 loop : -0.66 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 119 HIS 0.002 0.001 HIS A 436 PHE 0.017 0.001 PHE A 135 TYR 0.015 0.001 TYR A 161 ARG 0.006 0.000 ARG A 537 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1489.86 seconds wall clock time: 27 minutes 0.81 seconds (1620.81 seconds total)