Starting phenix.real_space_refine on Fri Nov 15 17:07:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ops_17086/11_2024/8ops_17086.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ops_17086/11_2024/8ops_17086.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/8ops_17086/11_2024/8ops_17086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ops_17086/11_2024/8ops_17086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ops_17086/11_2024/8ops_17086.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ops_17086/11_2024/8ops_17086.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= 0.001 sd= 0.018 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 69 5.49 5 S 19 5.16 5 C 2905 2.51 5 N 874 2.21 5 O 1115 1.98 5 H 4258 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9241 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6459 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 565 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 2216 Classifications: {'RNA': 69} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 31, 'rna3p_pyr': 25} Link IDs: {'rna2p': 12, 'rna3p': 56} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6508 SG CYS B 139 42.916 39.813 40.495 1.00130.08 S ATOM 6553 SG CYS B 142 46.905 37.913 39.572 1.00133.43 S ATOM 6674 SG CYS B 152 44.444 36.160 40.172 1.00129.36 S Time building chain proxies: 5.79, per 1000 atoms: 0.63 Number of scatterers: 9241 At special positions: 0 Unit cell: (79.05, 80.91, 134.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 19 16.00 P 69 15.00 O 1115 8.00 N 874 7.00 C 2905 6.00 H 4258 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 514.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 142 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 152 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 139 " 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 852 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 3 sheets defined 45.2% alpha, 8.3% beta 2 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 210 through 227 Processing helix chain 'A' and resid 255 through 265 Processing helix chain 'A' and resid 265 through 283 Processing helix chain 'A' and resid 288 through 306 Processing helix chain 'A' and resid 309 through 329 removed outlier: 4.247A pdb=" N HIS A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.538A pdb=" N CYS A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 Processing helix chain 'A' and resid 458 through 473 removed outlier: 3.995A pdb=" N PHE A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 463 " --> pdb=" O PRO A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 564 Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.664A pdb=" N LYS A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 630 Processing sheet with id=AA1, first strand: chain 'A' and resid 229 through 231 Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 338 removed outlier: 6.982A pdb=" N VAL A 397 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL A 385 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 503 removed outlier: 7.047A pdb=" N ILE A 508 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE A 502 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL A 506 " --> pdb=" O ILE A 502 " (cutoff:3.500A) 170 hydrogen bonds defined for protein. 492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4244 1.03 - 1.23: 36 1.23 - 1.42: 2335 1.42 - 1.62: 2852 1.62 - 1.81: 21 Bond restraints: 9488 Sorted by residual: bond pdb=" CB PRO A 287 " pdb=" CG PRO A 287 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 4.01e+00 bond pdb=" CA VAL A 434 " pdb=" CB VAL A 434 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.29e+00 bond pdb=" CA ASP B 137 " pdb=" CB ASP B 137 " ideal model delta sigma weight residual 1.532 1.550 -0.018 1.74e-02 3.30e+03 1.11e+00 bond pdb=" CA TRP A 509 " pdb=" CB TRP A 509 " ideal model delta sigma weight residual 1.535 1.554 -0.018 1.90e-02 2.77e+03 9.47e-01 bond pdb=" CG PRO B 158 " pdb=" CD PRO B 158 " ideal model delta sigma weight residual 1.503 1.472 0.031 3.40e-02 8.65e+02 8.11e-01 ... (remaining 9483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 16780 1.81 - 3.62: 363 3.62 - 5.43: 23 5.43 - 7.23: 0 7.23 - 9.04: 1 Bond angle restraints: 17167 Sorted by residual: angle pdb=" CA PRO A 287 " pdb=" N PRO A 287 " pdb=" CD PRO A 287 " ideal model delta sigma weight residual 112.00 106.99 5.01 1.40e+00 5.10e-01 1.28e+01 angle pdb=" CA LEU A 371 " pdb=" CB LEU A 371 " pdb=" CG LEU A 371 " ideal model delta sigma weight residual 116.30 125.34 -9.04 3.50e+00 8.16e-02 6.68e+00 angle pdb=" CA PRO B 158 " pdb=" N PRO B 158 " pdb=" CD PRO B 158 " ideal model delta sigma weight residual 112.00 108.48 3.52 1.40e+00 5.10e-01 6.34e+00 angle pdb=" C LEU A 370 " pdb=" N LEU A 371 " pdb=" CA LEU A 371 " ideal model delta sigma weight residual 120.31 116.53 3.78 1.52e+00 4.33e-01 6.18e+00 angle pdb=" C2' A C 69 " pdb=" C1' A C 69 " pdb=" N9 A C 69 " ideal model delta sigma weight residual 112.00 115.54 -3.54 1.50e+00 4.44e-01 5.57e+00 ... (remaining 17162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 3943 21.77 - 43.54: 362 43.54 - 65.32: 206 65.32 - 87.09: 29 87.09 - 108.86: 4 Dihedral angle restraints: 4544 sinusoidal: 3040 harmonic: 1504 Sorted by residual: dihedral pdb=" O4' C C 30 " pdb=" C1' C C 30 " pdb=" N1 C C 30 " pdb=" C2 C C 30 " ideal model delta sinusoidal sigma weight residual -128.00 -61.59 -66.41 1 1.70e+01 3.46e-03 1.99e+01 dihedral pdb=" O4' C C 18 " pdb=" C1' C C 18 " pdb=" N1 C C 18 " pdb=" C2 C C 18 " ideal model delta sinusoidal sigma weight residual -128.00 -65.76 -62.24 1 1.70e+01 3.46e-03 1.77e+01 dihedral pdb=" O4' U C 36 " pdb=" C1' U C 36 " pdb=" N1 U C 36 " pdb=" C2 U C 36 " ideal model delta sinusoidal sigma weight residual -160.00 -106.72 -53.28 1 1.50e+01 4.44e-03 1.72e+01 ... (remaining 4541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 739 0.043 - 0.085: 113 0.085 - 0.128: 37 0.128 - 0.170: 8 0.170 - 0.213: 1 Chirality restraints: 898 Sorted by residual: chirality pdb=" C1' A C 69 " pdb=" O4' A C 69 " pdb=" C2' A C 69 " pdb=" N9 A C 69 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB VAL A 385 " pdb=" CA VAL A 385 " pdb=" CG1 VAL A 385 " pdb=" CG2 VAL A 385 " both_signs ideal model delta sigma weight residual False -2.63 -2.79 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CB VAL A 556 " pdb=" CA VAL A 556 " pdb=" CG1 VAL A 556 " pdb=" CG2 VAL A 556 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 895 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 286 " 0.063 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO A 287 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 509 " -0.014 2.00e-02 2.50e+03 1.04e-02 4.32e+00 pdb=" CG TRP A 509 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 509 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 509 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 509 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 509 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 509 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 509 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 509 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 509 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 509 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP A 509 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 509 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 509 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 509 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 509 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 157 " 0.035 5.00e-02 4.00e+02 5.16e-02 4.27e+00 pdb=" N PRO B 158 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 158 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 158 " 0.029 5.00e-02 4.00e+02 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 383 2.18 - 2.79: 17078 2.79 - 3.39: 25080 3.39 - 4.00: 32305 4.00 - 4.60: 48572 Nonbonded interactions: 123418 Sorted by model distance: nonbonded pdb=" O MET A 465 " pdb=" HH TYR A 562 " model vdw 1.577 2.450 nonbonded pdb=" OE1 GLN A 546 " pdb=" H GLN A 546 " model vdw 1.665 2.450 nonbonded pdb=" O CYS A 447 " pdb=" HG SER A 448 " model vdw 1.705 2.450 nonbonded pdb=" OE2 GLU A 318 " pdb="HH21 ARG A 321 " model vdw 1.734 2.450 nonbonded pdb=" HZ1 LYS A 445 " pdb=" OD2 ASP A 450 " model vdw 1.738 2.450 ... (remaining 123413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.150 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.970 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5130 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 5230 Z= 0.176 Angle : 0.568 9.044 7421 Z= 0.301 Chirality : 0.038 0.213 898 Planarity : 0.006 0.093 692 Dihedral : 21.448 108.861 2407 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.78 % Allowed : 18.70 % Favored : 80.52 % 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: 1.99 (0.39), residues: 437 helix: 2.78 (0.37), residues: 190 sheet: 0.03 (0.77), residues: 38 loop : 0.26 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 509 HIS 0.013 0.002 HIS A 260 PHE 0.021 0.001 PHE A 469 TYR 0.009 0.001 TYR A 626 ARG 0.006 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 LYS cc_start: 0.6727 (mmmm) cc_final: 0.6418 (mmmm) REVERT: A 415 ASN cc_start: 0.8104 (m-40) cc_final: 0.7789 (t0) outliers start: 3 outliers final: 2 residues processed: 89 average time/residue: 0.4207 time to fit residues: 46.8603 Evaluate side-chains 78 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 373 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5394 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5230 Z= 0.202 Angle : 0.571 7.017 7421 Z= 0.303 Chirality : 0.039 0.210 898 Planarity : 0.006 0.046 692 Dihedral : 22.544 111.120 1544 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 2.08 % Allowed : 17.66 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.38), residues: 437 helix: 2.37 (0.37), residues: 191 sheet: -0.15 (0.77), residues: 43 loop : 0.02 (0.39), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 509 HIS 0.007 0.002 HIS A 329 PHE 0.010 0.001 PHE A 440 TYR 0.017 0.002 TYR A 562 ARG 0.005 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 HIS cc_start: 0.5619 (m170) cc_final: 0.5393 (m170) REVERT: A 331 LEU cc_start: 0.6388 (mm) cc_final: 0.6046 (mm) REVERT: A 369 LEU cc_start: 0.7810 (mt) cc_final: 0.7414 (mt) REVERT: A 378 ASN cc_start: 0.5822 (p0) cc_final: 0.5617 (p0) REVERT: A 415 ASN cc_start: 0.8102 (m-40) cc_final: 0.7842 (t0) outliers start: 8 outliers final: 5 residues processed: 88 average time/residue: 0.4901 time to fit residues: 52.1777 Evaluate side-chains 85 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 164 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5508 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5230 Z= 0.166 Angle : 0.512 6.035 7421 Z= 0.272 Chirality : 0.037 0.213 898 Planarity : 0.004 0.047 692 Dihedral : 22.479 111.594 1544 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.56 % Allowed : 17.40 % Favored : 81.04 % 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: 1.54 (0.39), residues: 437 helix: 2.24 (0.37), residues: 197 sheet: -0.20 (0.72), residues: 44 loop : 0.12 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 509 HIS 0.008 0.002 HIS A 262 PHE 0.013 0.001 PHE A 462 TYR 0.008 0.001 TYR A 626 ARG 0.002 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 HIS cc_start: 0.5918 (m170) cc_final: 0.5625 (m170) REVERT: A 275 LYS cc_start: 0.6833 (mmmm) cc_final: 0.6528 (mmmm) REVERT: A 369 LEU cc_start: 0.7855 (mt) cc_final: 0.7473 (mt) REVERT: A 415 ASN cc_start: 0.8091 (m-40) cc_final: 0.7839 (t0) outliers start: 6 outliers final: 4 residues processed: 86 average time/residue: 0.3410 time to fit residues: 35.2484 Evaluate side-chains 84 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 382 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 27 optimal weight: 0.1980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5549 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5230 Z= 0.148 Angle : 0.501 5.761 7421 Z= 0.265 Chirality : 0.036 0.219 898 Planarity : 0.004 0.046 692 Dihedral : 22.427 111.394 1542 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.34 % Allowed : 16.88 % Favored : 80.78 % 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: 1.52 (0.38), residues: 437 helix: 2.32 (0.37), residues: 191 sheet: -0.14 (0.74), residues: 44 loop : 0.05 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 555 HIS 0.003 0.001 HIS A 620 PHE 0.012 0.001 PHE A 462 TYR 0.008 0.001 TYR A 562 ARG 0.002 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 ASN cc_start: 0.8564 (m110) cc_final: 0.8324 (m110) REVERT: A 369 LEU cc_start: 0.7836 (mt) cc_final: 0.7462 (mt) REVERT: A 415 ASN cc_start: 0.8040 (m-40) cc_final: 0.7810 (t0) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.4771 time to fit residues: 46.3668 Evaluate side-chains 80 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 382 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.0020 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 5230 Z= 0.419 Angle : 0.719 5.870 7421 Z= 0.390 Chirality : 0.045 0.255 898 Planarity : 0.006 0.054 692 Dihedral : 22.930 111.997 1542 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.08 % Allowed : 19.48 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.37), residues: 437 helix: 0.88 (0.34), residues: 190 sheet: -0.55 (0.77), residues: 44 loop : -0.24 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP A 443 HIS 0.020 0.003 HIS A 260 PHE 0.024 0.002 PHE B 163 TYR 0.020 0.003 TYR A 562 ARG 0.005 0.001 ARG A 576 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7939 (m-80) cc_final: 0.7731 (m-80) REVERT: A 369 LEU cc_start: 0.8153 (mt) cc_final: 0.7942 (mt) REVERT: A 556 VAL cc_start: 0.5904 (t) cc_final: 0.5534 (m) outliers start: 8 outliers final: 5 residues processed: 87 average time/residue: 0.5434 time to fit residues: 56.3026 Evaluate side-chains 82 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 142 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 25 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5230 Z= 0.192 Angle : 0.552 6.406 7421 Z= 0.295 Chirality : 0.038 0.234 898 Planarity : 0.006 0.080 692 Dihedral : 22.751 112.729 1542 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.82 % Allowed : 21.56 % Favored : 76.62 % 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: 0.65 (0.39), residues: 437 helix: 1.63 (0.38), residues: 190 sheet: -0.97 (0.69), residues: 47 loop : -0.31 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 555 HIS 0.015 0.002 HIS A 260 PHE 0.019 0.002 PHE A 462 TYR 0.015 0.002 TYR A 626 ARG 0.006 0.000 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 HIS cc_start: 0.7129 (m90) cc_final: 0.6576 (m170) REVERT: A 312 ASN cc_start: 0.8665 (m110) cc_final: 0.8433 (m110) REVERT: A 327 PHE cc_start: 0.7797 (m-80) cc_final: 0.7317 (m-80) REVERT: A 369 LEU cc_start: 0.8081 (mt) cc_final: 0.7755 (mt) REVERT: A 556 VAL cc_start: 0.6067 (t) cc_final: 0.5660 (m) outliers start: 7 outliers final: 5 residues processed: 77 average time/residue: 0.5523 time to fit residues: 50.4856 Evaluate side-chains 79 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 380 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.0270 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.0270 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5230 Z= 0.214 Angle : 0.538 6.215 7421 Z= 0.288 Chirality : 0.037 0.232 898 Planarity : 0.005 0.076 692 Dihedral : 22.661 111.552 1542 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.30 % Allowed : 22.60 % Favored : 76.10 % 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: 0.64 (0.40), residues: 437 helix: 1.71 (0.37), residues: 190 sheet: -1.26 (0.67), residues: 47 loop : -0.35 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 555 HIS 0.022 0.003 HIS A 260 PHE 0.018 0.002 PHE A 462 TYR 0.020 0.002 TYR A 626 ARG 0.013 0.001 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.8652 (tpt) cc_final: 0.8281 (tpt) REVERT: A 327 PHE cc_start: 0.7633 (m-80) cc_final: 0.7310 (m-80) outliers start: 5 outliers final: 5 residues processed: 75 average time/residue: 0.5509 time to fit residues: 48.7262 Evaluate side-chains 75 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 380 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.0060 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.2572 ------------------------------------------------------------------------------- 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: 0.5899 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5230 Z= 0.147 Angle : 0.507 6.287 7421 Z= 0.268 Chirality : 0.036 0.243 898 Planarity : 0.005 0.077 692 Dihedral : 22.534 111.296 1542 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.82 % Allowed : 23.12 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.40), residues: 437 helix: 2.07 (0.38), residues: 190 sheet: -1.23 (0.66), residues: 47 loop : -0.18 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 555 HIS 0.009 0.001 HIS A 262 PHE 0.019 0.001 PHE A 462 TYR 0.015 0.001 TYR A 626 ARG 0.008 0.000 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLN cc_start: 0.6387 (tm-30) cc_final: 0.5519 (tt0) REVERT: A 323 MET cc_start: 0.8593 (tpt) cc_final: 0.8256 (tpt) REVERT: A 327 PHE cc_start: 0.7700 (m-80) cc_final: 0.7360 (m-80) outliers start: 7 outliers final: 6 residues processed: 76 average time/residue: 0.5622 time to fit residues: 50.2075 Evaluate side-chains 78 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 409 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.6378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 5230 Z= 0.324 Angle : 0.630 7.094 7421 Z= 0.340 Chirality : 0.041 0.238 898 Planarity : 0.006 0.086 692 Dihedral : 22.913 111.302 1539 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.82 % Allowed : 23.12 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.39), residues: 437 helix: 1.33 (0.37), residues: 190 sheet: -1.46 (0.68), residues: 46 loop : -0.60 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 443 HIS 0.022 0.003 HIS A 260 PHE 0.013 0.002 PHE A 468 TYR 0.016 0.003 TYR A 562 ARG 0.004 0.001 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 ARG cc_start: 0.7051 (ttm170) cc_final: 0.6604 (ttt90) outliers start: 7 outliers final: 5 residues processed: 76 average time/residue: 0.5653 time to fit residues: 50.5860 Evaluate side-chains 76 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 5 optimal weight: 0.0060 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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: 0.6021 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5230 Z= 0.176 Angle : 0.530 6.353 7421 Z= 0.283 Chirality : 0.037 0.251 898 Planarity : 0.005 0.084 692 Dihedral : 22.734 111.550 1539 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.04 % Allowed : 23.90 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.41), residues: 437 helix: 1.79 (0.38), residues: 190 sheet: -1.52 (0.66), residues: 46 loop : -0.40 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 555 HIS 0.009 0.001 HIS A 262 PHE 0.017 0.001 PHE A 462 TYR 0.016 0.002 TYR A 626 ARG 0.007 0.001 ARG A 441 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLN cc_start: 0.6520 (tm-30) cc_final: 0.5548 (tt0) REVERT: A 560 ARG cc_start: 0.7024 (ttm170) cc_final: 0.6574 (ttt90) outliers start: 4 outliers final: 4 residues processed: 81 average time/residue: 0.5696 time to fit residues: 54.3413 Evaluate side-chains 81 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 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 268 HIS ** 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 = 0.4500 r_free = 0.4500 target = 0.172421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.146693 restraints weight = 33413.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.152281 restraints weight = 17036.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.155828 restraints weight = 10095.707| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.6984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5230 Z= 0.251 Angle : 0.579 6.600 7421 Z= 0.311 Chirality : 0.039 0.253 898 Planarity : 0.006 0.087 692 Dihedral : 22.875 111.225 1539 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.04 % Allowed : 25.19 % Favored : 73.77 % 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: 0.36 (0.40), residues: 437 helix: 1.56 (0.38), residues: 190 sheet: -1.65 (0.66), residues: 46 loop : -0.53 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 555 HIS 0.014 0.002 HIS A 260 PHE 0.012 0.001 PHE A 462 TYR 0.017 0.002 TYR A 599 ARG 0.005 0.001 ARG A 441 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3661.69 seconds wall clock time: 69 minutes 28.14 seconds (4168.14 seconds total)