Starting phenix.real_space_refine on Thu Jul 18 22:26:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/07_2024/7sk2_25170.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/07_2024/7sk2_25170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/07_2024/7sk2_25170.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/07_2024/7sk2_25170.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/07_2024/7sk2_25170.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/07_2024/7sk2_25170.cif" } resolution = 3.82 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= 0.019 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 35 5.16 5 C 2788 2.51 5 N 651 2.21 5 O 703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4177 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4152 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 22, 'TRANS': 509} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'TGI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.31, per 1000 atoms: 0.79 Number of scatterers: 4177 At special positions: 0 Unit cell: (83.739, 73.17, 77.235, 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 35 16.00 O 703 8.00 N 651 7.00 C 2788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 818.3 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 75.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.559A pdb=" N MET A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 68 through 78 Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.927A pdb=" N LEU A 118 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 153 removed outlier: 4.167A pdb=" N GLY A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.758A pdb=" N CYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.646A pdb=" N TRP A 235 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.791A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 254 " --> pdb=" O MET A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.940A pdb=" N GLY A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 removed outlier: 4.106A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.585A pdb=" N ILE A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 315 through 349 removed outlier: 3.501A pdb=" N ASP A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 removed outlier: 3.522A pdb=" N VAL A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 363 through 374 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 410 removed outlier: 3.919A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 423 through 431 Processing helix chain 'A' and resid 431 through 440 removed outlier: 6.303A pdb=" N SER A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN A 438 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 454 Processing helix chain 'A' and resid 457 through 472 Processing helix chain 'A' and resid 476 through 489 removed outlier: 4.423A pdb=" N ASP A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 502 Processing helix chain 'A' and resid 502 through 518 Processing helix chain 'A' and resid 530 through 559 removed outlier: 3.559A pdb=" N SER A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) Proline residue: A 549 - end of helix Processing helix chain 'A' and resid 562 through 569 removed outlier: 4.235A pdb=" N ARG A 566 " --> pdb=" O SER A 562 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 524 256 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1211 1.34 - 1.46: 1142 1.46 - 1.58: 1904 1.58 - 1.70: 4 1.70 - 1.82: 52 Bond restraints: 4313 Sorted by residual: bond pdb=" C03 TGI A 601 " pdb=" C07 TGI A 601 " ideal model delta sigma weight residual 1.468 1.538 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C03 TGI A 601 " pdb=" S04 TGI A 601 " ideal model delta sigma weight residual 1.744 1.690 0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" C07 TGI A 601 " pdb=" C20 TGI A 601 " ideal model delta sigma weight residual 1.480 1.531 -0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" C20 TGI A 601 " pdb=" S24 TGI A 601 " ideal model delta sigma weight residual 1.737 1.687 0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" C14 TGI A 601 " pdb=" C15 TGI A 601 " ideal model delta sigma weight residual 1.539 1.494 0.045 2.00e-02 2.50e+03 4.98e+00 ... (remaining 4308 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.34: 101 105.34 - 112.56: 2047 112.56 - 119.78: 1558 119.78 - 127.01: 2098 127.01 - 134.23: 79 Bond angle restraints: 5883 Sorted by residual: angle pdb=" C ILE A 377 " pdb=" N SER A 378 " pdb=" CA SER A 378 " ideal model delta sigma weight residual 120.58 127.09 -6.51 1.32e+00 5.74e-01 2.43e+01 angle pdb=" CB LYS A 350 " pdb=" CG LYS A 350 " pdb=" CD LYS A 350 " ideal model delta sigma weight residual 111.30 122.26 -10.96 2.30e+00 1.89e-01 2.27e+01 angle pdb=" CA VAL A 58 " pdb=" CB VAL A 58 " pdb=" CG1 VAL A 58 " ideal model delta sigma weight residual 110.40 117.16 -6.76 1.70e+00 3.46e-01 1.58e+01 angle pdb=" C SER A 302 " pdb=" N LEU A 303 " pdb=" CA LEU A 303 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C LEU A 416 " pdb=" N ARG A 417 " pdb=" CA ARG A 417 " ideal model delta sigma weight residual 122.06 115.23 6.83 1.86e+00 2.89e-01 1.35e+01 ... (remaining 5878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 2204 16.93 - 33.86: 179 33.86 - 50.80: 45 50.80 - 67.73: 4 67.73 - 84.66: 4 Dihedral angle restraints: 2436 sinusoidal: 906 harmonic: 1530 Sorted by residual: dihedral pdb=" CA PHE A 480 " pdb=" C PHE A 480 " pdb=" N TYR A 481 " pdb=" CA TYR A 481 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA GLN A 199 " pdb=" C GLN A 199 " pdb=" N MET A 200 " pdb=" CA MET A 200 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ALA A 130 " pdb=" C ALA A 130 " pdb=" N VAL A 131 " pdb=" CA VAL A 131 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 2433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 379 0.039 - 0.079: 170 0.079 - 0.118: 60 0.118 - 0.157: 24 0.157 - 0.197: 9 Chirality restraints: 642 Sorted by residual: chirality pdb=" CB VAL A 546 " pdb=" CA VAL A 546 " pdb=" CG1 VAL A 546 " pdb=" CG2 VAL A 546 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CB ILE A 341 " pdb=" CA ILE A 341 " pdb=" CG1 ILE A 341 " pdb=" CG2 ILE A 341 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA SER A 378 " pdb=" N SER A 378 " pdb=" C SER A 378 " pdb=" CB SER A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.06e-01 ... (remaining 639 not shown) Planarity restraints: 722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 137 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ASN A 137 " 0.057 2.00e-02 2.50e+03 pdb=" O ASN A 137 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE A 138 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 136 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C LEU A 136 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU A 136 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN A 137 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 138 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.09e+00 pdb=" C ILE A 138 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE A 138 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 139 " 0.017 2.00e-02 2.50e+03 ... (remaining 719 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 815 2.77 - 3.30: 4247 3.30 - 3.83: 7327 3.83 - 4.37: 8299 4.37 - 4.90: 13716 Nonbonded interactions: 34404 Sorted by model distance: nonbonded pdb=" OH TYR A 296 " pdb=" OG SER A 328 " model vdw 2.235 2.440 nonbonded pdb=" O VAL A 142 " pdb=" OG SER A 145 " model vdw 2.250 2.440 nonbonded pdb=" O PHE A 92 " pdb=" OG1 THR A 504 " model vdw 2.264 2.440 nonbonded pdb=" O PHE A 450 " pdb=" OG SER A 454 " model vdw 2.265 2.440 nonbonded pdb=" O SER A 437 " pdb=" OG1 THR A 440 " model vdw 2.285 2.440 ... (remaining 34399 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: 0.680 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.790 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 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 0.070 4313 Z= 0.338 Angle : 1.059 10.959 5883 Z= 0.545 Chirality : 0.055 0.197 642 Planarity : 0.006 0.044 722 Dihedral : 13.666 84.661 1461 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.34), residues: 530 helix: -1.32 (0.26), residues: 346 sheet: None (None), residues: 0 loop : -2.27 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 230 HIS 0.001 0.000 HIS A 347 PHE 0.037 0.003 PHE A 480 TYR 0.039 0.003 TYR A 452 ARG 0.005 0.001 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.7822 (tmm) cc_final: 0.7527 (tmm) REVERT: A 283 GLU cc_start: 0.8133 (pp20) cc_final: 0.7926 (pp20) REVERT: A 292 ILE cc_start: 0.8583 (mm) cc_final: 0.8317 (mm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1355 time to fit residues: 23.5490 Evaluate side-chains 110 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 483 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4313 Z= 0.227 Angle : 0.702 8.002 5883 Z= 0.364 Chirality : 0.042 0.136 642 Planarity : 0.005 0.033 722 Dihedral : 6.693 45.644 599 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.11 % Allowed : 13.15 % Favored : 84.74 % 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: -1.65 (0.37), residues: 530 helix: -0.66 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -1.82 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 230 HIS 0.008 0.002 HIS A 347 PHE 0.017 0.002 PHE A 462 TYR 0.026 0.002 TYR A 139 ARG 0.004 0.001 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8280 (m-40) cc_final: 0.7697 (m-40) REVERT: A 200 MET cc_start: 0.6738 (tpt) cc_final: 0.6325 (mmm) REVERT: A 283 GLU cc_start: 0.8272 (pp20) cc_final: 0.7507 (pp20) REVERT: A 287 ASP cc_start: 0.7965 (m-30) cc_final: 0.7649 (m-30) REVERT: A 479 ARG cc_start: 0.7625 (ptt180) cc_final: 0.7397 (ptt180) REVERT: A 527 TYR cc_start: 0.7640 (t80) cc_final: 0.7388 (t80) REVERT: A 545 MET cc_start: 0.8391 (mmt) cc_final: 0.8136 (mmt) outliers start: 9 outliers final: 9 residues processed: 129 average time/residue: 0.1232 time to fit residues: 20.8800 Evaluate side-chains 125 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 526 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4313 Z= 0.251 Angle : 0.695 7.863 5883 Z= 0.358 Chirality : 0.043 0.141 642 Planarity : 0.004 0.029 722 Dihedral : 6.498 44.781 599 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.29 % Allowed : 16.43 % Favored : 80.28 % 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: -1.24 (0.37), residues: 530 helix: -0.34 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.62 (0.51), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 168 HIS 0.009 0.003 HIS A 347 PHE 0.023 0.002 PHE A 385 TYR 0.022 0.002 TYR A 152 ARG 0.003 0.001 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8253 (m-40) cc_final: 0.7743 (m-40) REVERT: A 174 PHE cc_start: 0.6493 (p90) cc_final: 0.5675 (p90) REVERT: A 198 HIS cc_start: 0.7556 (m90) cc_final: 0.7353 (m90) REVERT: A 283 GLU cc_start: 0.8292 (pp20) cc_final: 0.7574 (pp20) REVERT: A 287 ASP cc_start: 0.8056 (m-30) cc_final: 0.7481 (m-30) REVERT: A 479 ARG cc_start: 0.7665 (ptt180) cc_final: 0.7432 (ptt180) REVERT: A 527 TYR cc_start: 0.7806 (t80) cc_final: 0.7564 (t80) outliers start: 14 outliers final: 12 residues processed: 131 average time/residue: 0.1269 time to fit residues: 21.7616 Evaluate side-chains 135 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 526 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.0270 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4313 Z= 0.184 Angle : 0.645 7.305 5883 Z= 0.332 Chirality : 0.041 0.201 642 Planarity : 0.004 0.027 722 Dihedral : 6.279 43.900 599 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.05 % Allowed : 18.78 % Favored : 78.17 % 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: -0.92 (0.38), residues: 530 helix: -0.09 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.53 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 168 HIS 0.009 0.002 HIS A 347 PHE 0.019 0.002 PHE A 385 TYR 0.020 0.002 TYR A 139 ARG 0.002 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.480 Fit side-chains REVERT: A 77 ASN cc_start: 0.8265 (m-40) cc_final: 0.7780 (m-40) REVERT: A 168 TRP cc_start: 0.6069 (p90) cc_final: 0.5836 (p90) REVERT: A 283 GLU cc_start: 0.8249 (pp20) cc_final: 0.7604 (pp20) REVERT: A 287 ASP cc_start: 0.7977 (m-30) cc_final: 0.7401 (m-30) REVERT: A 452 TYR cc_start: 0.7977 (t80) cc_final: 0.7576 (t80) REVERT: A 479 ARG cc_start: 0.7584 (ptt180) cc_final: 0.7322 (ptt180) outliers start: 13 outliers final: 10 residues processed: 126 average time/residue: 0.1297 time to fit residues: 21.3649 Evaluate side-chains 128 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 46 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 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4313 Z= 0.196 Angle : 0.670 8.520 5883 Z= 0.342 Chirality : 0.042 0.171 642 Planarity : 0.004 0.026 722 Dihedral : 6.145 43.035 599 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.46 % Allowed : 20.42 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.38), residues: 530 helix: 0.03 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.46 (0.53), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 193 HIS 0.009 0.002 HIS A 347 PHE 0.023 0.002 PHE A 404 TYR 0.019 0.002 TYR A 139 ARG 0.001 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8302 (m-40) cc_final: 0.7821 (m-40) REVERT: A 168 TRP cc_start: 0.5973 (p90) cc_final: 0.5751 (p90) REVERT: A 198 HIS cc_start: 0.7277 (m90) cc_final: 0.7018 (m-70) REVERT: A 200 MET cc_start: 0.6858 (tpt) cc_final: 0.6453 (mmm) REVERT: A 283 GLU cc_start: 0.8254 (pp20) cc_final: 0.7597 (pp20) REVERT: A 287 ASP cc_start: 0.8002 (m-30) cc_final: 0.7393 (m-30) REVERT: A 452 TYR cc_start: 0.7978 (t80) cc_final: 0.7580 (t80) REVERT: A 479 ARG cc_start: 0.7623 (ptt180) cc_final: 0.7347 (ptt180) REVERT: A 545 MET cc_start: 0.8298 (mmt) cc_final: 0.8065 (mmt) outliers start: 19 outliers final: 16 residues processed: 129 average time/residue: 0.1284 time to fit residues: 21.8241 Evaluate side-chains 134 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.0870 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 438 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4313 Z= 0.178 Angle : 0.648 7.317 5883 Z= 0.334 Chirality : 0.041 0.216 642 Planarity : 0.004 0.026 722 Dihedral : 6.005 42.610 599 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.93 % Allowed : 21.36 % Favored : 73.71 % 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: -0.59 (0.38), residues: 530 helix: 0.17 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.43 (0.53), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.009 0.002 HIS A 347 PHE 0.021 0.001 PHE A 385 TYR 0.020 0.001 TYR A 139 ARG 0.002 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8328 (m-40) cc_final: 0.7855 (m-40) REVERT: A 200 MET cc_start: 0.6779 (tpt) cc_final: 0.6397 (mmm) REVERT: A 283 GLU cc_start: 0.8270 (pp20) cc_final: 0.7618 (pp20) REVERT: A 287 ASP cc_start: 0.7961 (m-30) cc_final: 0.7300 (m-30) REVERT: A 452 TYR cc_start: 0.7925 (t80) cc_final: 0.7529 (t80) outliers start: 21 outliers final: 16 residues processed: 133 average time/residue: 0.1304 time to fit residues: 22.6428 Evaluate side-chains 135 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4313 Z= 0.201 Angle : 0.700 9.156 5883 Z= 0.355 Chirality : 0.042 0.199 642 Planarity : 0.004 0.026 722 Dihedral : 5.987 42.003 599 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.46 % Allowed : 22.77 % Favored : 72.77 % 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: -0.51 (0.38), residues: 530 helix: 0.23 (0.28), residues: 354 sheet: None (None), residues: 0 loop : -1.37 (0.53), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 193 HIS 0.008 0.003 HIS A 347 PHE 0.032 0.002 PHE A 404 TYR 0.020 0.001 TYR A 139 ARG 0.001 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8354 (m-40) cc_final: 0.7899 (m-40) REVERT: A 200 MET cc_start: 0.6839 (tpt) cc_final: 0.6434 (mmm) REVERT: A 283 GLU cc_start: 0.8295 (pp20) cc_final: 0.7640 (pp20) REVERT: A 287 ASP cc_start: 0.8012 (m-30) cc_final: 0.7340 (m-30) REVERT: A 452 TYR cc_start: 0.7963 (t80) cc_final: 0.7545 (t80) REVERT: A 462 PHE cc_start: 0.8413 (t80) cc_final: 0.8143 (t80) REVERT: A 479 ARG cc_start: 0.7575 (ptt180) cc_final: 0.7304 (ptt180) REVERT: A 487 MET cc_start: 0.6936 (tpp) cc_final: 0.5759 (tpp) outliers start: 19 outliers final: 16 residues processed: 125 average time/residue: 0.1310 time to fit residues: 21.4726 Evaluate side-chains 132 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4313 Z= 0.219 Angle : 0.715 10.048 5883 Z= 0.364 Chirality : 0.043 0.190 642 Planarity : 0.004 0.026 722 Dihedral : 6.070 41.125 599 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.99 % Allowed : 23.94 % Favored : 72.07 % 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 (0.38), residues: 530 helix: 0.17 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -1.20 (0.53), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 193 HIS 0.010 0.003 HIS A 347 PHE 0.021 0.002 PHE A 404 TYR 0.022 0.002 TYR A 139 ARG 0.002 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8391 (m-40) cc_final: 0.7958 (m-40) REVERT: A 174 PHE cc_start: 0.6351 (p90) cc_final: 0.5487 (p90) REVERT: A 283 GLU cc_start: 0.8402 (pp20) cc_final: 0.7767 (pp20) REVERT: A 287 ASP cc_start: 0.8057 (m-30) cc_final: 0.7376 (m-30) REVERT: A 452 TYR cc_start: 0.8006 (t80) cc_final: 0.7562 (t80) outliers start: 17 outliers final: 16 residues processed: 127 average time/residue: 0.1350 time to fit residues: 22.2379 Evaluate side-chains 134 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.0030 chunk 37 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4313 Z= 0.196 Angle : 0.708 8.577 5883 Z= 0.362 Chirality : 0.043 0.186 642 Planarity : 0.004 0.027 722 Dihedral : 6.029 40.682 599 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.23 % Allowed : 23.94 % Favored : 71.83 % 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: -0.41 (0.38), residues: 530 helix: 0.23 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -1.16 (0.54), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 168 HIS 0.009 0.002 HIS A 347 PHE 0.016 0.001 PHE A 385 TYR 0.022 0.001 TYR A 139 ARG 0.002 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8184 (m110) cc_final: 0.7779 (m-40) REVERT: A 174 PHE cc_start: 0.6194 (p90) cc_final: 0.5328 (p90) REVERT: A 200 MET cc_start: 0.6911 (tpt) cc_final: 0.6555 (mmm) REVERT: A 283 GLU cc_start: 0.8351 (pp20) cc_final: 0.7705 (pp20) REVERT: A 287 ASP cc_start: 0.7964 (m-30) cc_final: 0.7403 (m-30) REVERT: A 462 PHE cc_start: 0.8593 (t80) cc_final: 0.8335 (t80) outliers start: 18 outliers final: 15 residues processed: 125 average time/residue: 0.1323 time to fit residues: 21.6287 Evaluate side-chains 130 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 chunk 6 optimal weight: 3.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 153 ASN A 438 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4313 Z= 0.213 Angle : 0.756 11.846 5883 Z= 0.381 Chirality : 0.045 0.238 642 Planarity : 0.004 0.026 722 Dihedral : 6.062 40.068 599 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.52 % Allowed : 26.06 % Favored : 70.42 % 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: -0.46 (0.38), residues: 530 helix: 0.20 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -1.17 (0.53), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 168 HIS 0.009 0.002 HIS A 347 PHE 0.034 0.002 PHE A 404 TYR 0.029 0.002 TYR A 551 ARG 0.001 0.000 ARG A 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8390 (m-40) cc_final: 0.8022 (m-40) REVERT: A 174 PHE cc_start: 0.6134 (p90) cc_final: 0.5350 (p90) REVERT: A 200 MET cc_start: 0.6955 (tpt) cc_final: 0.6524 (mmm) REVERT: A 283 GLU cc_start: 0.8413 (pp20) cc_final: 0.7782 (pp20) REVERT: A 287 ASP cc_start: 0.8050 (m-30) cc_final: 0.7396 (m-30) REVERT: A 479 ARG cc_start: 0.7566 (ptt180) cc_final: 0.7291 (ptt180) outliers start: 15 outliers final: 15 residues processed: 124 average time/residue: 0.1220 time to fit residues: 20.0652 Evaluate side-chains 132 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.0070 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.162530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.140957 restraints weight = 9243.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.144446 restraints weight = 5658.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.146827 restraints weight = 3995.704| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4313 Z= 0.192 Angle : 0.745 11.226 5883 Z= 0.376 Chirality : 0.044 0.237 642 Planarity : 0.004 0.027 722 Dihedral : 5.964 39.849 599 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.52 % Allowed : 27.00 % Favored : 69.48 % 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: -0.38 (0.38), residues: 530 helix: 0.27 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -1.20 (0.54), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 168 HIS 0.009 0.002 HIS A 347 PHE 0.019 0.001 PHE A 385 TYR 0.023 0.001 TYR A 139 ARG 0.001 0.000 ARG A 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1207.12 seconds wall clock time: 23 minutes 40.81 seconds (1420.81 seconds total)