Starting phenix.real_space_refine on Sun Aug 4 02:52:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9biu_44602/08_2024/9biu_44602_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9biu_44602/08_2024/9biu_44602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9biu_44602/08_2024/9biu_44602.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9biu_44602/08_2024/9biu_44602.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9biu_44602/08_2024/9biu_44602_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9biu_44602/08_2024/9biu_44602_trim.cif" } resolution = 2.9 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= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 C 3105 2.51 5 N 767 2.21 5 O 813 1.98 5 H 4738 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A ASP 317": "OD1" <-> "OD2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B ASP 73": "OD1" <-> "OD2" 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: 9458 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7539 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 472, 7529 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 21, 'TRANS': 450} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 472, 7529 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 21, 'TRANS': 450} Chain breaks: 1 bond proxies already assigned to first conformer: 7620 Chain: "B" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1890 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CXN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.10, per 1000 atoms: 0.86 Number of scatterers: 9458 At special positions: 0 Unit cell: (86.376, 110.532, 83.448, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 O 813 8.00 N 767 7.00 C 3105 6.00 H 4738 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.81 Conformation dependent library (CDL) restraints added in 1.5 seconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1106 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 2 sheets defined 63.4% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 46 through 74 removed outlier: 5.003A pdb=" N ASN A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 107 Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 112 through 131 Processing helix chain 'A' and resid 140 through 170 removed outlier: 4.192A pdb=" N GLY A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Proline residue: A 162 - end of helix removed outlier: 3.697A pdb=" N ALA A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 206 removed outlier: 3.584A pdb=" N ARG A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Proline residue: A 203 - end of helix removed outlier: 3.615A pdb=" N ARG A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 238 removed outlier: 3.990A pdb=" N ALA A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) Proline residue: A 224 - end of helix removed outlier: 3.767A pdb=" N GLY A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 250 through 266 removed outlier: 3.845A pdb=" N ARG A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.826A pdb=" N ASP A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.645A pdb=" N PHE A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 329 removed outlier: 3.525A pdb=" N LEU A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 346 through 362 removed outlier: 3.587A pdb=" N PHE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Proline residue: A 357 - end of helix Processing helix chain 'A' and resid 362 through 370 removed outlier: 3.800A pdb=" N CYS A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 403 Processing helix chain 'A' and resid 611 through 636 removed outlier: 3.660A pdb=" N THR A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 631 " --> pdb=" O VAL A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 641 through 665 removed outlier: 3.548A pdb=" N LEU A 645 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 646 " --> pdb=" O LYS A 642 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 695 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 53 through 56 removed outlier: 4.270A pdb=" N ARG B 56 " --> pdb=" O TRP B 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 110 through 114 Processing sheet with id=AA1, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.621A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N MET B 34 " --> pdb=" O SER B 50 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 797 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: 2.90 Time building geometry restraints manager: 7.24 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: 4729 1.04 - 1.24: 637 1.24 - 1.44: 1486 1.44 - 1.64: 2681 1.64 - 1.84: 55 Bond restraints: 9588 Sorted by residual: bond pdb=" N25 CXN A 801 " pdb=" O24 CXN A 801 " ideal model delta sigma weight residual 1.363 1.418 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" N VAL B 87 " pdb=" H VAL B 87 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 6.93e+00 bond pdb=" N VAL B 87 " pdb=" CA VAL B 87 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.23e-02 6.61e+03 5.39e+00 bond pdb=" C6 CXN A 801 " pdb=" C8 CXN A 801 " ideal model delta sigma weight residual 1.546 1.510 0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" C2 CXN A 801 " pdb=" N2 CXN A 801 " ideal model delta sigma weight residual 1.421 1.455 -0.034 2.00e-02 2.50e+03 2.94e+00 ... (remaining 9583 not shown) Histogram of bond angle deviations from ideal: 84.98 - 95.19: 5 95.19 - 105.41: 91 105.41 - 115.63: 11965 115.63 - 125.84: 5140 125.84 - 136.06: 117 Bond angle restraints: 17318 Sorted by residual: angle pdb=" CA GLN A 278 " pdb=" CB GLN A 278 " pdb=" CG GLN A 278 " ideal model delta sigma weight residual 114.10 122.07 -7.97 2.00e+00 2.50e-01 1.59e+01 angle pdb=" N PRO B 88 " pdb=" CA PRO B 88 " pdb=" C PRO B 88 " ideal model delta sigma weight residual 113.75 109.70 4.05 1.49e+00 4.50e-01 7.38e+00 angle pdb=" N ASP A 273 " pdb=" CA ASP A 273 " pdb=" C ASP A 273 " ideal model delta sigma weight residual 113.18 109.62 3.56 1.33e+00 5.65e-01 7.18e+00 angle pdb=" N GLN A 278 " pdb=" CA GLN A 278 " pdb=" C GLN A 278 " ideal model delta sigma weight residual 113.28 109.19 4.09 1.57e+00 4.06e-01 6.80e+00 angle pdb=" N THR A 96 " pdb=" CA THR A 96 " pdb=" C THR A 96 " ideal model delta sigma weight residual 109.81 115.30 -5.49 2.21e+00 2.05e-01 6.18e+00 ... (remaining 17313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 3974 17.61 - 35.22: 391 35.22 - 52.82: 140 52.82 - 70.43: 40 70.43 - 88.04: 4 Dihedral angle restraints: 4549 sinusoidal: 2406 harmonic: 2143 Sorted by residual: dihedral pdb=" CA TRP A 283 " pdb=" C TRP A 283 " pdb=" N ALA A 284 " pdb=" CA ALA A 284 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLY A 159 " pdb=" C GLY A 159 " pdb=" N ILE A 160 " pdb=" CA ILE A 160 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LYS A 110 " pdb=" C LYS A 110 " pdb=" N PHE A 111 " pdb=" CA PHE A 111 " ideal model delta harmonic sigma weight residual -180.00 -160.37 -19.63 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 4546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 619 0.047 - 0.094: 98 0.094 - 0.142: 20 0.142 - 0.189: 1 0.189 - 0.236: 1 Chirality restraints: 739 Sorted by residual: chirality pdb=" CA VAL B 87 " pdb=" N VAL B 87 " pdb=" C VAL B 87 " pdb=" CB VAL B 87 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE A 49 " pdb=" N ILE A 49 " pdb=" C ILE A 49 " pdb=" CB ILE A 49 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ILE A 133 " pdb=" N ILE A 133 " pdb=" C ILE A 133 " pdb=" CB ILE A 133 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 736 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C26 CXN A 801 " -0.036 2.00e-02 2.50e+03 1.94e-02 7.54e+00 pdb=" C28 CXN A 801 " 0.022 2.00e-02 2.50e+03 pdb=" C29 CXN A 801 " 0.006 2.00e-02 2.50e+03 pdb=" C30 CXN A 801 " -0.015 2.00e-02 2.50e+03 pdb=" C31 CXN A 801 " -0.016 2.00e-02 2.50e+03 pdb=" C32 CXN A 801 " 0.002 2.00e-02 2.50e+03 pdb=" C33 CXN A 801 " 0.023 2.00e-02 2.50e+03 pdb="CL CXN A 801 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 278 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C GLN A 278 " -0.037 2.00e-02 2.50e+03 pdb=" O GLN A 278 " 0.014 2.00e-02 2.50e+03 pdb=" N HIS A 279 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 307 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.42e+00 pdb=" N PRO A 308 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " -0.029 5.00e-02 4.00e+02 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 910 2.23 - 2.82: 20649 2.82 - 3.42: 24921 3.42 - 4.01: 34102 4.01 - 4.60: 52430 Nonbonded interactions: 133012 Sorted by model distance: nonbonded pdb=" O TRP B 53 " pdb=" HG SER B 54 " model vdw 1.639 2.450 nonbonded pdb=" O HIS A 76 " pdb=" H THR B 108 " model vdw 1.680 2.450 nonbonded pdb=" OD1 ASP A 170 " pdb=" HH TYR A 634 " model vdw 1.695 2.450 nonbonded pdb=" HE ARG B 45 " pdb=" OE2 GLU B 111 " model vdw 1.700 2.450 nonbonded pdb=" O ARG A 266 " pdb=" H ARG A 268 " model vdw 1.703 2.450 ... (remaining 133007 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 29.740 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 33.270 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 0.055 4849 Z= 0.170 Angle : 0.562 7.969 6594 Z= 0.301 Chirality : 0.037 0.236 739 Planarity : 0.004 0.053 816 Dihedral : 17.103 88.040 1730 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.00 % Allowed : 23.95 % Favored : 74.05 % 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: 0.77 (0.36), residues: 590 helix: 1.97 (0.29), residues: 341 sheet: -0.96 (0.72), residues: 59 loop : -1.79 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 107 HIS 0.001 0.000 HIS A 279 PHE 0.009 0.001 PHE A 48 TYR 0.008 0.001 TYR A 183 ARG 0.002 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 1.7282 time to fit residues: 140.9185 Evaluate side-chains 74 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 25 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.0030 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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: 0.8288 moved from start: 0.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4849 Z= 0.238 Angle : 0.582 7.136 6594 Z= 0.308 Chirality : 0.039 0.149 739 Planarity : 0.004 0.051 816 Dihedral : 7.415 57.080 691 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.59 % Allowed : 22.16 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.35), residues: 590 helix: 1.88 (0.28), residues: 339 sheet: -1.17 (0.69), residues: 59 loop : -1.83 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.003 0.001 HIS A 291 PHE 0.022 0.002 PHE A 48 TYR 0.015 0.001 TYR A 634 ARG 0.002 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 198 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8184 (p) REVERT: A 374 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.8086 (m-10) REVERT: B 56 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7473 (mtp180) REVERT: B 106 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.7705 (ptpt) outliers start: 18 outliers final: 6 residues processed: 79 average time/residue: 1.7959 time to fit residues: 150.0291 Evaluate side-chains 77 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.0570 chunk 40 optimal weight: 0.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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: 0.8301 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4849 Z= 0.255 Angle : 0.579 7.020 6594 Z= 0.305 Chirality : 0.039 0.150 739 Planarity : 0.005 0.050 816 Dihedral : 7.158 56.960 687 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.79 % Allowed : 23.15 % Favored : 74.05 % 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: 0.50 (0.35), residues: 590 helix: 1.80 (0.28), residues: 339 sheet: -1.31 (0.69), residues: 59 loop : -1.87 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.003 0.001 HIS A 291 PHE 0.023 0.001 PHE A 48 TYR 0.012 0.001 TYR A 634 ARG 0.003 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7680 (tt) REVERT: A 198 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8197 (p) REVERT: A 374 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8080 (m-10) REVERT: B 56 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7462 (mtp180) REVERT: B 106 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7954 (ptpt) outliers start: 14 outliers final: 5 residues processed: 74 average time/residue: 1.9728 time to fit residues: 153.5429 Evaluate side-chains 73 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8324 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4849 Z= 0.309 Angle : 0.605 7.056 6594 Z= 0.321 Chirality : 0.040 0.151 739 Planarity : 0.005 0.051 816 Dihedral : 7.089 43.379 686 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.59 % Allowed : 22.75 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.35), residues: 590 helix: 1.55 (0.28), residues: 344 sheet: -1.52 (0.67), residues: 59 loop : -1.83 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.005 0.001 HIS A 279 PHE 0.026 0.002 PHE A 48 TYR 0.013 0.002 TYR A 634 ARG 0.003 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7708 (tt) REVERT: A 198 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.8167 (p) REVERT: A 374 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.8116 (m-10) REVERT: B 38 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8059 (ptp-170) REVERT: B 56 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7491 (mtp180) REVERT: B 106 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.7974 (ptpt) outliers start: 18 outliers final: 7 residues processed: 82 average time/residue: 2.0649 time to fit residues: 177.4621 Evaluate side-chains 77 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 108 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4849 Z= 0.264 Angle : 0.592 6.948 6594 Z= 0.314 Chirality : 0.039 0.149 739 Planarity : 0.005 0.051 816 Dihedral : 6.939 43.754 685 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.79 % Allowed : 23.35 % Favored : 72.85 % 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: 0.29 (0.35), residues: 590 helix: 1.58 (0.28), residues: 345 sheet: -1.57 (0.67), residues: 59 loop : -1.91 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.004 0.001 HIS A 279 PHE 0.024 0.002 PHE A 48 TYR 0.012 0.001 TYR A 634 ARG 0.003 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7691 (tt) REVERT: A 198 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.8185 (p) REVERT: A 211 CYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7057 (m) REVERT: A 374 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.8097 (m-10) REVERT: B 38 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8050 (ptp-170) REVERT: B 56 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7502 (mtp180) REVERT: B 106 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.7846 (ptpt) outliers start: 19 outliers final: 6 residues processed: 82 average time/residue: 2.0526 time to fit residues: 176.6967 Evaluate side-chains 73 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8323 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4849 Z= 0.290 Angle : 0.607 6.928 6594 Z= 0.323 Chirality : 0.040 0.150 739 Planarity : 0.005 0.052 816 Dihedral : 6.951 43.523 685 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.39 % Allowed : 22.95 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.34), residues: 590 helix: 1.54 (0.28), residues: 345 sheet: -1.60 (0.67), residues: 59 loop : -1.93 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.004 0.001 HIS A 279 PHE 0.025 0.002 PHE A 48 TYR 0.013 0.001 TYR A 634 ARG 0.002 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7686 (tt) REVERT: A 198 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8146 (p) REVERT: A 211 CYS cc_start: 0.7336 (OUTLIER) cc_final: 0.7055 (m) REVERT: A 374 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: B 38 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8055 (ptp-170) REVERT: B 56 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7499 (mtp180) REVERT: B 106 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.7892 (ptpt) outliers start: 22 outliers final: 10 residues processed: 82 average time/residue: 1.8805 time to fit residues: 162.8717 Evaluate side-chains 78 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 123 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 31 optimal weight: 0.0870 chunk 56 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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: 0.8287 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4849 Z= 0.191 Angle : 0.571 7.264 6594 Z= 0.303 Chirality : 0.038 0.147 739 Planarity : 0.005 0.050 816 Dihedral : 6.621 43.520 685 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.19 % Allowed : 23.95 % Favored : 72.85 % 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: 0.49 (0.35), residues: 590 helix: 1.76 (0.28), residues: 345 sheet: -1.47 (0.68), residues: 59 loop : -1.86 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.000 HIS A 279 PHE 0.019 0.001 PHE A 48 TYR 0.010 0.001 TYR A 634 ARG 0.002 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8135 (p) REVERT: A 211 CYS cc_start: 0.7233 (OUTLIER) cc_final: 0.7009 (m) REVERT: A 374 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8062 (m-10) REVERT: B 56 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7492 (mtp180) REVERT: B 79 MET cc_start: 0.8571 (ttp) cc_final: 0.8300 (ttp) REVERT: B 106 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7966 (ptpt) outliers start: 16 outliers final: 7 residues processed: 78 average time/residue: 2.1727 time to fit residues: 177.4765 Evaluate side-chains 73 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 123 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4849 Z= 0.225 Angle : 0.581 7.277 6594 Z= 0.309 Chirality : 0.038 0.148 739 Planarity : 0.005 0.051 816 Dihedral : 6.562 42.875 685 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.59 % Allowed : 25.55 % Favored : 71.86 % 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: 0.48 (0.35), residues: 590 helix: 1.75 (0.28), residues: 345 sheet: -1.54 (0.67), residues: 59 loop : -1.84 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.003 0.001 HIS A 279 PHE 0.021 0.001 PHE A 48 TYR 0.012 0.001 TYR A 634 ARG 0.006 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 198 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8126 (p) REVERT: A 211 CYS cc_start: 0.7257 (OUTLIER) cc_final: 0.7023 (m) REVERT: A 374 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8068 (m-10) REVERT: B 56 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7504 (mtp180) REVERT: B 106 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8060 (ptpt) outliers start: 13 outliers final: 6 residues processed: 71 average time/residue: 1.7949 time to fit residues: 134.7412 Evaluate side-chains 71 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4849 Z= 0.260 Angle : 0.595 7.622 6594 Z= 0.316 Chirality : 0.039 0.149 739 Planarity : 0.005 0.050 816 Dihedral : 6.343 42.714 681 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.39 % Allowed : 24.75 % Favored : 71.86 % 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: 0.42 (0.35), residues: 590 helix: 1.70 (0.28), residues: 345 sheet: -1.60 (0.67), residues: 59 loop : -1.84 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.003 0.001 HIS A 279 PHE 0.023 0.002 PHE A 48 TYR 0.012 0.001 TYR A 634 ARG 0.003 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7634 (tt) REVERT: A 198 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8116 (p) REVERT: A 211 CYS cc_start: 0.7276 (OUTLIER) cc_final: 0.7047 (m) REVERT: A 278 GLN cc_start: 0.7323 (tp40) cc_final: 0.6947 (tp40) REVERT: A 374 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.8108 (m-10) REVERT: B 56 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7505 (mtp180) REVERT: B 106 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7935 (ptpt) outliers start: 17 outliers final: 8 residues processed: 77 average time/residue: 1.8035 time to fit residues: 146.5756 Evaluate side-chains 75 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.9990 chunk 46 optimal weight: 0.0050 chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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: 0.8287 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4849 Z= 0.195 Angle : 0.572 7.409 6594 Z= 0.303 Chirality : 0.038 0.147 739 Planarity : 0.005 0.050 816 Dihedral : 6.166 42.943 681 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.79 % Allowed : 25.15 % Favored : 72.06 % 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: 0.56 (0.35), residues: 590 helix: 1.82 (0.28), residues: 345 sheet: -1.53 (0.67), residues: 59 loop : -1.80 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.003 0.001 HIS A 279 PHE 0.019 0.001 PHE A 48 TYR 0.011 0.001 TYR A 634 ARG 0.002 0.000 ARG B 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7616 (tt) REVERT: A 198 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8113 (p) REVERT: A 211 CYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6983 (m) REVERT: A 278 GLN cc_start: 0.7316 (tp40) cc_final: 0.6930 (tp40) REVERT: A 374 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.8046 (m-10) REVERT: B 56 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7513 (mtp180) REVERT: B 106 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8086 (ptpt) REVERT: B 115 GLU cc_start: 0.8280 (pt0) cc_final: 0.7940 (mp0) outliers start: 14 outliers final: 7 residues processed: 74 average time/residue: 1.8238 time to fit residues: 142.5964 Evaluate side-chains 74 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 48 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.0010 chunk 40 optimal weight: 0.1980 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.168079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.135546 restraints weight = 18826.863| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.37 r_work: 0.3652 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4849 Z= 0.162 Angle : 0.554 7.392 6594 Z= 0.294 Chirality : 0.037 0.146 739 Planarity : 0.005 0.050 816 Dihedral : 5.948 42.904 681 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.99 % Allowed : 24.75 % Favored : 72.26 % 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: 0.81 (0.36), residues: 590 helix: 2.13 (0.29), residues: 334 sheet: -1.41 (0.68), residues: 59 loop : -1.72 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 107 HIS 0.002 0.000 HIS A 279 PHE 0.015 0.001 PHE A 48 TYR 0.010 0.001 TYR A 634 ARG 0.002 0.000 ARG B 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4575.17 seconds wall clock time: 80 minutes 23.56 seconds (4823.56 seconds total)