Starting phenix.real_space_refine on Fri Aug 2 17:12:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/08_2024/8tzs_41768.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/08_2024/8tzs_41768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/08_2024/8tzs_41768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/08_2024/8tzs_41768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/08_2024/8tzs_41768.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzs_41768/08_2024/8tzs_41768.cif" } resolution = 3.84 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 2594 2.51 5 N 637 2.21 5 O 647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A ASP 180": "OD1" <-> "OD2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3914 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3914 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 20, 'TRANS': 459} Chain breaks: 2 Time building chain proxies: 3.11, per 1000 atoms: 0.79 Number of scatterers: 3914 At special positions: 0 Unit cell: (86.346, 103.32, 78.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 647 8.00 N 637 7.00 C 2594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 179 " distance=2.04 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: 1.46 Conformation dependent library (CDL) restraints added in 671.4 milliseconds 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 902 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 54.4% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 10 through 36 removed outlier: 3.868A pdb=" N ILE A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 removed outlier: 4.043A pdb=" N GLN A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 227 through 258 removed outlier: 3.588A pdb=" N LYS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Proline residue: A 243 - end of helix Processing helix chain 'A' and resid 264 through 282 removed outlier: 3.630A pdb=" N PHE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 286 through 291 removed outlier: 4.112A pdb=" N GLY A 290 " --> pdb=" O TRP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 322 removed outlier: 3.708A pdb=" N ASP A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 334 Processing helix chain 'A' and resid 335 through 360 Proline residue: A 341 - end of helix removed outlier: 3.753A pdb=" N VAL A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE A 352 " --> pdb=" O CYS A 348 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 413 removed outlier: 3.611A pdb=" N SER A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 456 Processing helix chain 'A' and resid 473 through 493 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 46 removed outlier: 5.976A pdb=" N ILE A 216 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA A 119 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N MET A 110 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU A 186 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE A 112 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.991A pdb=" N MET A 134 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ARG A 155 " --> pdb=" O MET A 134 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 136 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N HIS A 153 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 138 " --> pdb=" O MET A 151 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 633 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: 0.95 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1185 1.35 - 1.46: 1036 1.46 - 1.58: 1747 1.58 - 1.70: 2 1.70 - 1.81: 60 Bond restraints: 4030 Sorted by residual: bond pdb=" CB PRO A 263 " pdb=" CG PRO A 263 " ideal model delta sigma weight residual 1.492 1.667 -0.175 5.00e-02 4.00e+02 1.22e+01 bond pdb=" CG PRO A 263 " pdb=" CD PRO A 263 " ideal model delta sigma weight residual 1.503 1.390 0.113 3.40e-02 8.65e+02 1.10e+01 bond pdb=" N PRO A 263 " pdb=" CD PRO A 263 " ideal model delta sigma weight residual 1.473 1.514 -0.041 1.40e-02 5.10e+03 8.64e+00 bond pdb=" N PRO A 263 " pdb=" CA PRO A 263 " ideal model delta sigma weight residual 1.465 1.444 0.020 1.11e-02 8.12e+03 3.36e+00 bond pdb=" CB PRO A 170 " pdb=" CG PRO A 170 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.08e+00 ... (remaining 4025 not shown) Histogram of bond angle deviations from ideal: 93.36 - 101.99: 24 101.99 - 110.62: 1146 110.62 - 119.25: 2164 119.25 - 127.87: 2067 127.87 - 136.50: 56 Bond angle restraints: 5457 Sorted by residual: angle pdb=" CA PRO A 263 " pdb=" N PRO A 263 " pdb=" CD PRO A 263 " ideal model delta sigma weight residual 112.00 95.97 16.03 1.40e+00 5.10e-01 1.31e+02 angle pdb=" N PRO A 263 " pdb=" CD PRO A 263 " pdb=" CG PRO A 263 " ideal model delta sigma weight residual 103.20 93.36 9.84 1.50e+00 4.44e-01 4.30e+01 angle pdb=" CA PRO A 170 " pdb=" N PRO A 170 " pdb=" CD PRO A 170 " ideal model delta sigma weight residual 112.00 105.41 6.59 1.40e+00 5.10e-01 2.22e+01 angle pdb=" CA LEU A 440 " pdb=" CB LEU A 440 " pdb=" CG LEU A 440 " ideal model delta sigma weight residual 116.30 131.82 -15.52 3.50e+00 8.16e-02 1.97e+01 angle pdb=" CA CYS A 179 " pdb=" CB CYS A 179 " pdb=" SG CYS A 179 " ideal model delta sigma weight residual 114.40 124.10 -9.70 2.30e+00 1.89e-01 1.78e+01 ... (remaining 5452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 2018 16.01 - 32.02: 233 32.02 - 48.04: 78 48.04 - 64.05: 10 64.05 - 80.06: 5 Dihedral angle restraints: 2344 sinusoidal: 951 harmonic: 1393 Sorted by residual: dihedral pdb=" CA CYS A 179 " pdb=" C CYS A 179 " pdb=" N ASP A 180 " pdb=" CA ASP A 180 " ideal model delta harmonic sigma weight residual -180.00 -131.97 -48.03 0 5.00e+00 4.00e-02 9.23e+01 dihedral pdb=" CA LYS A 161 " pdb=" C LYS A 161 " pdb=" N CYS A 162 " pdb=" CA CYS A 162 " ideal model delta harmonic sigma weight residual 180.00 -148.29 -31.71 0 5.00e+00 4.00e-02 4.02e+01 dihedral pdb=" CA GLU A 178 " pdb=" C GLU A 178 " pdb=" N CYS A 179 " pdb=" CA CYS A 179 " ideal model delta harmonic sigma weight residual 180.00 -157.47 -22.53 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 2341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 457 0.053 - 0.106: 128 0.106 - 0.158: 8 0.158 - 0.211: 1 0.211 - 0.264: 3 Chirality restraints: 597 Sorted by residual: chirality pdb=" CB ILE A 216 " pdb=" CA ILE A 216 " pdb=" CG1 ILE A 216 " pdb=" CG2 ILE A 216 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA CYS A 179 " pdb=" N CYS A 179 " pdb=" C CYS A 179 " pdb=" CB CYS A 179 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO A 263 " pdb=" N PRO A 263 " pdb=" C PRO A 263 " pdb=" CB PRO A 263 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 594 not shown) Planarity restraints: 672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 169 " 0.070 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO A 170 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 262 " -0.068 5.00e-02 4.00e+02 9.20e-02 1.35e+01 pdb=" N PRO A 263 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 263 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 263 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 490 " 0.010 2.00e-02 2.50e+03 1.10e-02 2.12e+00 pdb=" CG PHE A 490 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 490 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 490 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 490 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 490 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 490 " 0.001 2.00e-02 2.50e+03 ... (remaining 669 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 155 2.72 - 3.26: 4179 3.26 - 3.81: 6425 3.81 - 4.35: 7251 4.35 - 4.90: 12405 Nonbonded interactions: 30415 Sorted by model distance: nonbonded pdb=" OD1 ASN A 8 " pdb=" OG SER A 495 " model vdw 2.170 3.040 nonbonded pdb=" NH1 ARG A 158 " pdb=" O PRO A 183 " model vdw 2.171 3.120 nonbonded pdb=" O MET A 9 " pdb=" NH2 ARG A 431 " model vdw 2.174 3.120 nonbonded pdb=" O THR A 371 " pdb=" N GLY A 374 " model vdw 2.234 3.120 nonbonded pdb=" O GLN A 326 " pdb=" NH1 ARG A 329 " model vdw 2.289 3.120 ... (remaining 30410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.420 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.005 0.175 4030 Z= 0.323 Angle : 0.871 16.031 5457 Z= 0.477 Chirality : 0.047 0.264 597 Planarity : 0.007 0.103 672 Dihedral : 15.830 80.062 1436 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.24 % Allowed : 20.57 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: 0.65 (0.38), residues: 474 helix: 1.37 (0.32), residues: 223 sheet: 0.18 (0.61), residues: 67 loop : -0.56 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 66 HIS 0.004 0.001 HIS A 192 PHE 0.026 0.002 PHE A 490 TYR 0.016 0.002 TYR A 45 ARG 0.002 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7109 (mm-30) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.1312 time to fit residues: 16.5992 Evaluate side-chains 92 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.0770 chunk 36 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4030 Z= 0.211 Angle : 0.649 10.594 5457 Z= 0.337 Chirality : 0.045 0.256 597 Planarity : 0.005 0.060 672 Dihedral : 5.384 40.040 511 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.55 % Allowed : 17.97 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 0.96 (0.38), residues: 474 helix: 1.55 (0.32), residues: 229 sheet: 0.46 (0.61), residues: 67 loop : -0.44 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 192 PHE 0.016 0.002 PHE A 318 TYR 0.012 0.002 TYR A 45 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 TYR cc_start: 0.7982 (t80) cc_final: 0.7641 (t80) outliers start: 15 outliers final: 12 residues processed: 111 average time/residue: 0.1412 time to fit residues: 20.6059 Evaluate side-chains 107 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 439 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7608 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4030 Z= 0.197 Angle : 0.622 13.049 5457 Z= 0.318 Chirality : 0.043 0.198 597 Planarity : 0.004 0.046 672 Dihedral : 5.079 37.344 511 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.73 % Allowed : 18.44 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 1.24 (0.39), residues: 474 helix: 1.82 (0.33), residues: 229 sheet: 0.60 (0.58), residues: 67 loop : -0.35 (0.51), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 192 PHE 0.016 0.002 PHE A 490 TYR 0.017 0.001 TYR A 45 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 MET cc_start: 0.8417 (mmm) cc_final: 0.8211 (mmm) REVERT: A 478 TYR cc_start: 0.8042 (t80) cc_final: 0.7751 (t80) REVERT: A 489 MET cc_start: 0.8862 (mtm) cc_final: 0.8637 (mtm) outliers start: 20 outliers final: 17 residues processed: 110 average time/residue: 0.1258 time to fit residues: 17.8729 Evaluate side-chains 112 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 331 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4030 Z= 0.206 Angle : 0.625 11.731 5457 Z= 0.314 Chirality : 0.043 0.153 597 Planarity : 0.004 0.036 672 Dihedral : 4.922 32.636 511 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.67 % Allowed : 19.62 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 1.39 (0.39), residues: 474 helix: 1.98 (0.33), residues: 228 sheet: 0.57 (0.56), residues: 74 loop : -0.32 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 66 HIS 0.003 0.001 HIS A 496 PHE 0.023 0.002 PHE A 490 TYR 0.011 0.001 TYR A 140 ARG 0.003 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8533 (pt) REVERT: A 259 MET cc_start: 0.8419 (mmm) cc_final: 0.8200 (mmm) REVERT: A 432 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.6173 (t80) REVERT: A 478 TYR cc_start: 0.8019 (t80) cc_final: 0.7747 (t80) outliers start: 24 outliers final: 17 residues processed: 112 average time/residue: 0.1293 time to fit residues: 18.6635 Evaluate side-chains 112 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 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: 0.7625 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4030 Z= 0.203 Angle : 0.640 14.356 5457 Z= 0.317 Chirality : 0.042 0.130 597 Planarity : 0.004 0.033 672 Dihedral : 4.849 29.545 511 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 6.38 % Allowed : 20.33 % Favored : 73.29 % 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: 1.47 (0.39), residues: 474 helix: 1.95 (0.33), residues: 230 sheet: 0.78 (0.58), residues: 74 loop : -0.24 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 66 HIS 0.003 0.001 HIS A 496 PHE 0.021 0.002 PHE A 490 TYR 0.028 0.002 TYR A 140 ARG 0.003 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6175 (t80) REVERT: A 489 MET cc_start: 0.8775 (mtm) cc_final: 0.8394 (mtm) outliers start: 27 outliers final: 20 residues processed: 115 average time/residue: 0.1360 time to fit residues: 19.9347 Evaluate side-chains 113 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 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 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4030 Z= 0.183 Angle : 0.630 13.184 5457 Z= 0.311 Chirality : 0.042 0.132 597 Planarity : 0.004 0.031 672 Dihedral : 4.759 26.643 511 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.91 % Allowed : 21.28 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.39), residues: 474 helix: 2.05 (0.33), residues: 230 sheet: 1.27 (0.65), residues: 61 loop : -0.32 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 148 HIS 0.003 0.001 HIS A 496 PHE 0.017 0.002 PHE A 490 TYR 0.025 0.002 TYR A 140 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8159 (ptp) cc_final: 0.7644 (pmm) REVERT: A 310 MET cc_start: 0.8391 (tpt) cc_final: 0.8166 (tpp) REVERT: A 406 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7326 (t0) REVERT: A 432 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.6160 (t80) REVERT: A 489 MET cc_start: 0.8836 (mtm) cc_final: 0.8609 (mtm) outliers start: 25 outliers final: 20 residues processed: 121 average time/residue: 0.1282 time to fit residues: 19.9502 Evaluate side-chains 121 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 9 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7606 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4030 Z= 0.186 Angle : 0.639 14.822 5457 Z= 0.314 Chirality : 0.042 0.134 597 Planarity : 0.004 0.038 672 Dihedral : 4.721 25.543 511 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.15 % Allowed : 22.46 % Favored : 71.39 % 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: 1.60 (0.38), residues: 474 helix: 2.03 (0.33), residues: 230 sheet: 1.26 (0.64), residues: 63 loop : -0.26 (0.48), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 66 HIS 0.003 0.001 HIS A 496 PHE 0.022 0.002 PHE A 490 TYR 0.013 0.002 TYR A 45 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 323 MET cc_start: 0.7667 (mmt) cc_final: 0.7351 (mtt) REVERT: A 432 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6131 (t80) REVERT: A 489 MET cc_start: 0.8847 (mtm) cc_final: 0.8636 (mtm) outliers start: 26 outliers final: 22 residues processed: 119 average time/residue: 0.1317 time to fit residues: 20.0181 Evaluate side-chains 123 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4030 Z= 0.172 Angle : 0.637 14.484 5457 Z= 0.312 Chirality : 0.042 0.149 597 Planarity : 0.004 0.040 672 Dihedral : 4.654 23.907 511 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 6.38 % Allowed : 20.80 % Favored : 72.81 % 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: 1.71 (0.39), residues: 474 helix: 2.10 (0.32), residues: 230 sheet: 1.38 (0.64), residues: 61 loop : -0.17 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 66 HIS 0.003 0.000 HIS A 496 PHE 0.019 0.001 PHE A 490 TYR 0.021 0.002 TYR A 392 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 101 MET cc_start: 0.8166 (ptp) cc_final: 0.7651 (pmm) REVERT: A 145 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7980 (p90) REVERT: A 281 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8377 (t0) REVERT: A 406 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7310 (t0) REVERT: A 432 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.6104 (t80) outliers start: 27 outliers final: 18 residues processed: 124 average time/residue: 0.1284 time to fit residues: 20.4430 Evaluate side-chains 126 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 477 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 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 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4030 Z= 0.198 Angle : 0.655 15.020 5457 Z= 0.324 Chirality : 0.043 0.158 597 Planarity : 0.004 0.040 672 Dihedral : 4.650 23.497 511 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 6.38 % Allowed : 21.51 % Favored : 72.10 % 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: 1.61 (0.38), residues: 474 helix: 1.99 (0.32), residues: 230 sheet: 1.34 (0.64), residues: 61 loop : -0.18 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 66 HIS 0.003 0.001 HIS A 496 PHE 0.023 0.002 PHE A 490 TYR 0.018 0.002 TYR A 392 ARG 0.003 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 101 MET cc_start: 0.8174 (ptp) cc_final: 0.7649 (pmm) REVERT: A 150 GLU cc_start: 0.7046 (tt0) cc_final: 0.6844 (tt0) REVERT: A 281 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8400 (t0) REVERT: A 406 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7269 (t0) REVERT: A 432 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6118 (t80) outliers start: 27 outliers final: 22 residues processed: 125 average time/residue: 0.1294 time to fit residues: 20.8761 Evaluate side-chains 131 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 477 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4030 Z= 0.203 Angle : 0.664 15.605 5457 Z= 0.328 Chirality : 0.043 0.135 597 Planarity : 0.004 0.041 672 Dihedral : 4.607 22.451 511 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.91 % Allowed : 22.22 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.39), residues: 474 helix: 1.95 (0.32), residues: 230 sheet: 0.96 (0.57), residues: 76 loop : -0.01 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 66 HIS 0.003 0.001 HIS A 496 PHE 0.029 0.002 PHE A 490 TYR 0.017 0.002 TYR A 392 ARG 0.002 0.000 ARG A 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 101 MET cc_start: 0.8165 (ptp) cc_final: 0.7635 (pmm) REVERT: A 281 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8373 (t0) REVERT: A 406 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7677 (t0) REVERT: A 478 TYR cc_start: 0.8126 (t80) cc_final: 0.7842 (t80) outliers start: 25 outliers final: 22 residues processed: 123 average time/residue: 0.1327 time to fit residues: 20.8761 Evaluate side-chains 131 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 477 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** 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 = 0.4013 r_free = 0.4013 target = 0.156330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.128189 restraints weight = 8308.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131561 restraints weight = 4946.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133922 restraints weight = 3482.170| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4030 Z= 0.218 Angle : 0.675 15.848 5457 Z= 0.335 Chirality : 0.043 0.130 597 Planarity : 0.004 0.040 672 Dihedral : 4.656 23.753 511 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.67 % Allowed : 21.99 % Favored : 72.34 % 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: 1.59 (0.39), residues: 474 helix: 1.99 (0.33), residues: 229 sheet: 0.90 (0.56), residues: 75 loop : -0.12 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 66 HIS 0.002 0.000 HIS A 153 PHE 0.020 0.002 PHE A 398 TYR 0.016 0.002 TYR A 392 ARG 0.003 0.000 ARG A 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1206.25 seconds wall clock time: 22 minutes 10.15 seconds (1330.15 seconds total)