Starting phenix.real_space_refine on Tue Feb 13 05:17:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6l_33643/02_2024/7y6l_33643.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6l_33643/02_2024/7y6l_33643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6l_33643/02_2024/7y6l_33643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6l_33643/02_2024/7y6l_33643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6l_33643/02_2024/7y6l_33643.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6l_33643/02_2024/7y6l_33643.pdb" } resolution = 3.5 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= 0.008 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 16 5.16 5 C 2115 2.51 5 N 556 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 57": "OD1" <-> "OD2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 104": "OD1" <-> "OD2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3308 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1519 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 953 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.34, per 1000 atoms: 0.71 Number of scatterers: 3308 At special positions: 0 Unit cell: (101.967, 72.952, 66.32, 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 16 16.00 O 621 8.00 N 556 7.00 C 2115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 634.0 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 8.5% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.140A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.722A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.063A pdb=" N LEU H 18 " --> pdb=" O TRP H 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.324A pdb=" N TRP H 33 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP H 57 " --> pdb=" O HIS H 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.795A pdb=" N CYS H 96 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TRP H 112 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG H 98 " --> pdb=" O HIS H 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.450A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 113 hydrogen bonds defined for protein. 261 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1037 1.35 - 1.48: 969 1.48 - 1.60: 1371 1.60 - 1.73: 0 1.73 - 1.85: 20 Bond restraints: 3397 Sorted by residual: bond pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 1.808 1.850 -0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CB VAL A 350 " pdb=" CG1 VAL A 350 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.34e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.34e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" C3 NAG A1301 " pdb=" O3 NAG A1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.63e-01 ... (remaining 3392 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.76: 100 106.76 - 113.57: 1795 113.57 - 120.37: 1216 120.37 - 127.17: 1467 127.17 - 133.97: 40 Bond angle restraints: 4618 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 123.11 -8.71 2.30e+00 1.89e-01 1.43e+01 angle pdb=" C LYS L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.11e+00 angle pdb=" C VAL A 350 " pdb=" CA VAL A 350 " pdb=" CB VAL A 350 " ideal model delta sigma weight residual 112.26 109.09 3.17 1.62e+00 3.81e-01 3.83e+00 angle pdb=" N VAL A 350 " pdb=" CA VAL A 350 " pdb=" C VAL A 350 " ideal model delta sigma weight residual 111.09 113.30 -2.21 1.25e+00 6.40e-01 3.14e+00 angle pdb=" CA TYR L 91 " pdb=" CB TYR L 91 " pdb=" CG TYR L 91 " ideal model delta sigma weight residual 113.90 117.09 -3.19 1.80e+00 3.09e-01 3.13e+00 ... (remaining 4613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 1741 17.68 - 35.37: 211 35.37 - 53.05: 44 53.05 - 70.73: 8 70.73 - 88.42: 2 Dihedral angle restraints: 2006 sinusoidal: 785 harmonic: 1221 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 47.13 45.87 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 50.37 42.63 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CA CYS A 432 " pdb=" C CYS A 432 " pdb=" N VAL A 433 " pdb=" CA VAL A 433 " ideal model delta harmonic sigma weight residual -180.00 -163.73 -16.27 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 337 0.039 - 0.079: 113 0.079 - 0.118: 46 0.118 - 0.157: 2 0.157 - 0.197: 1 Chirality restraints: 499 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 496 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " 0.034 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO A 384 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 76 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C ILE H 76 " -0.022 2.00e-02 2.50e+03 pdb=" O ILE H 76 " 0.008 2.00e-02 2.50e+03 pdb=" N THR H 77 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 511 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.08e+00 pdb=" C VAL A 511 " -0.018 2.00e-02 2.50e+03 pdb=" O VAL A 511 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL A 512 " 0.006 2.00e-02 2.50e+03 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 255 2.74 - 3.28: 3095 3.28 - 3.82: 5294 3.82 - 4.36: 6181 4.36 - 4.90: 11199 Nonbonded interactions: 26024 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.198 2.440 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.223 2.440 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.240 2.440 nonbonded pdb=" O SER A 443 " pdb=" NH1 ARG H 59 " model vdw 2.251 2.520 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.296 2.440 ... (remaining 26019 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: 0.160 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: 0.980 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.270 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 : 0.004 0.042 3397 Z= 0.231 Angle : 0.540 8.708 4618 Z= 0.286 Chirality : 0.045 0.197 499 Planarity : 0.004 0.052 586 Dihedral : 15.592 88.416 1214 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.56 % Allowed : 24.79 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.30 (0.42), residues: 416 helix: -3.39 (0.77), residues: 27 sheet: 0.90 (0.45), residues: 153 loop : -0.53 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS H 110 PHE 0.011 0.001 PHE A 392 TYR 0.015 0.001 TYR L 91 ARG 0.004 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.488 Fit side-chains REVERT: A 357 ARG cc_start: 0.7266 (ttt-90) cc_final: 0.6858 (ttm-80) REVERT: A 403 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7560 (mtp180) REVERT: A 471 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6402 (mm-30) REVERT: H 17 SER cc_start: 0.8227 (m) cc_final: 0.7955 (p) REVERT: H 19 MET cc_start: 0.7052 (ttm) cc_final: 0.6608 (ttp) REVERT: H 21 SER cc_start: 0.7327 (p) cc_final: 0.7057 (t) REVERT: L 69 THR cc_start: 0.7509 (p) cc_final: 0.7144 (m) outliers start: 2 outliers final: 2 residues processed: 52 average time/residue: 0.1570 time to fit residues: 10.1122 Evaluate side-chains 39 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 105 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.0010 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 0.0970 chunk 37 optimal weight: 5.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN H 67 HIS L 6 GLN L 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3397 Z= 0.136 Angle : 0.476 7.681 4618 Z= 0.252 Chirality : 0.044 0.201 499 Planarity : 0.003 0.040 586 Dihedral : 5.199 47.876 488 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.35 % Allowed : 22.82 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.13 (0.42), residues: 416 helix: -2.81 (0.86), residues: 27 sheet: 0.91 (0.45), residues: 158 loop : -0.42 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.002 0.001 HIS H 110 PHE 0.007 0.001 PHE A 392 TYR 0.010 0.001 TYR L 91 ARG 0.002 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 40 time to evaluate : 0.358 Fit side-chains REVERT: A 357 ARG cc_start: 0.7186 (ttt-90) cc_final: 0.6735 (ttm-80) REVERT: A 462 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6251 (mmtm) REVERT: A 471 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6478 (mm-30) REVERT: H 17 SER cc_start: 0.8257 (m) cc_final: 0.7988 (p) REVERT: H 19 MET cc_start: 0.7062 (ttm) cc_final: 0.6689 (ttp) REVERT: H 21 SER cc_start: 0.7258 (p) cc_final: 0.7021 (t) REVERT: H 91 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7258 (t) REVERT: L 5 THR cc_start: 0.7361 (m) cc_final: 0.6617 (t) outliers start: 19 outliers final: 11 residues processed: 58 average time/residue: 0.1452 time to fit residues: 10.6313 Evaluate side-chains 48 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 35 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 0.0970 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 0.0010 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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: 0.7169 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3397 Z= 0.119 Angle : 0.456 7.028 4618 Z= 0.239 Chirality : 0.043 0.188 499 Planarity : 0.003 0.036 586 Dihedral : 5.041 53.865 487 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.92 % Allowed : 22.25 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.01 (0.42), residues: 416 helix: -2.52 (0.92), residues: 27 sheet: 0.98 (0.44), residues: 158 loop : -0.35 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.001 0.000 HIS H 110 PHE 0.006 0.001 PHE A 392 TYR 0.010 0.001 TYR L 91 ARG 0.002 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 35 time to evaluate : 0.387 Fit side-chains REVERT: A 357 ARG cc_start: 0.7178 (ttt-90) cc_final: 0.6758 (ttm-80) REVERT: A 462 LYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6303 (mmtm) REVERT: A 471 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6487 (mm-30) REVERT: H 10 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.4770 (mp0) REVERT: H 17 SER cc_start: 0.8244 (m) cc_final: 0.7999 (p) REVERT: H 19 MET cc_start: 0.7168 (ttm) cc_final: 0.6781 (ttp) REVERT: H 21 SER cc_start: 0.7229 (p) cc_final: 0.7029 (t) REVERT: L 5 THR cc_start: 0.7370 (m) cc_final: 0.6647 (t) outliers start: 21 outliers final: 8 residues processed: 56 average time/residue: 0.1340 time to fit residues: 9.6298 Evaluate side-chains 46 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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: 0.7236 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3397 Z= 0.231 Angle : 0.532 8.755 4618 Z= 0.276 Chirality : 0.046 0.205 499 Planarity : 0.004 0.033 586 Dihedral : 4.750 34.463 486 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.63 % Allowed : 21.69 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.05 (0.42), residues: 416 helix: -2.47 (0.95), residues: 27 sheet: 1.19 (0.45), residues: 150 loop : -0.54 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.001 0.000 HIS H 110 PHE 0.010 0.001 PHE L 71 TYR 0.015 0.001 TYR L 91 ARG 0.002 0.000 ARG H 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 35 time to evaluate : 0.381 Fit side-chains REVERT: A 357 ARG cc_start: 0.7228 (ttt-90) cc_final: 0.6874 (ttm-80) REVERT: A 462 LYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6341 (mmtm) REVERT: H 10 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.4883 (mp0) REVERT: H 19 MET cc_start: 0.7203 (ttm) cc_final: 0.6821 (ttp) REVERT: H 21 SER cc_start: 0.7210 (p) cc_final: 0.6986 (t) outliers start: 20 outliers final: 14 residues processed: 55 average time/residue: 0.1534 time to fit residues: 10.5037 Evaluate side-chains 48 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 32 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 0.0270 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- 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: 0.7243 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3397 Z= 0.228 Angle : 0.532 9.280 4618 Z= 0.276 Chirality : 0.046 0.205 499 Planarity : 0.004 0.031 586 Dihedral : 4.838 35.629 486 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 7.04 % Allowed : 21.41 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.13 (0.41), residues: 416 helix: -2.58 (0.91), residues: 27 sheet: 1.13 (0.44), residues: 150 loop : -0.57 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.002 0.000 HIS H 110 PHE 0.009 0.001 PHE A 347 TYR 0.013 0.001 TYR L 91 ARG 0.003 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 36 time to evaluate : 0.373 Fit side-chains REVERT: A 357 ARG cc_start: 0.7205 (ttt-90) cc_final: 0.6907 (ttm-80) REVERT: A 462 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6294 (mmtm) REVERT: H 10 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.4888 (mp0) REVERT: H 19 MET cc_start: 0.7268 (ttm) cc_final: 0.6856 (ttp) REVERT: H 39 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6628 (tt0) outliers start: 25 outliers final: 18 residues processed: 60 average time/residue: 0.1420 time to fit residues: 10.7592 Evaluate side-chains 56 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 35 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 0.0040 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3397 Z= 0.220 Angle : 0.533 9.298 4618 Z= 0.275 Chirality : 0.046 0.254 499 Planarity : 0.004 0.031 586 Dihedral : 5.079 43.206 486 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 7.04 % Allowed : 21.97 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.14 (0.42), residues: 416 helix: -2.52 (0.93), residues: 27 sheet: 1.10 (0.44), residues: 151 loop : -0.59 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.001 0.001 HIS H 110 PHE 0.008 0.001 PHE A 347 TYR 0.013 0.001 TYR L 91 ARG 0.003 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 34 time to evaluate : 0.375 Fit side-chains REVERT: A 357 ARG cc_start: 0.7204 (ttt-90) cc_final: 0.6946 (ttm-80) REVERT: A 462 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6297 (mmtm) REVERT: H 10 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.4875 (mp0) REVERT: H 19 MET cc_start: 0.7225 (ttm) cc_final: 0.6739 (ttp) REVERT: H 39 GLN cc_start: 0.6981 (OUTLIER) cc_final: 0.6607 (tt0) outliers start: 25 outliers final: 20 residues processed: 56 average time/residue: 0.1313 time to fit residues: 9.4683 Evaluate side-chains 56 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 33 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 0.0020 chunk 25 optimal weight: 3.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- 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: 0.7226 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3397 Z= 0.177 Angle : 0.513 8.852 4618 Z= 0.266 Chirality : 0.045 0.213 499 Planarity : 0.003 0.033 586 Dihedral : 5.103 46.046 486 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 6.48 % Allowed : 22.82 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.42), residues: 416 helix: -2.41 (0.93), residues: 27 sheet: 1.12 (0.44), residues: 151 loop : -0.52 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.002 0.001 HIS H 110 PHE 0.008 0.001 PHE H 109 TYR 0.011 0.001 TYR L 91 ARG 0.003 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 34 time to evaluate : 0.390 Fit side-chains REVERT: A 357 ARG cc_start: 0.7207 (ttt-90) cc_final: 0.6930 (ttm-80) REVERT: A 462 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6312 (mmtm) REVERT: H 10 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.4738 (mp0) REVERT: H 19 MET cc_start: 0.7223 (ttm) cc_final: 0.6729 (ttp) outliers start: 23 outliers final: 18 residues processed: 56 average time/residue: 0.1339 time to fit residues: 9.6025 Evaluate side-chains 51 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 31 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 35 optimal weight: 0.0770 chunk 37 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3397 Z= 0.138 Angle : 0.501 8.419 4618 Z= 0.261 Chirality : 0.045 0.200 499 Planarity : 0.003 0.033 586 Dihedral : 5.520 55.091 486 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.79 % Allowed : 25.35 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.08 (0.43), residues: 416 helix: -2.35 (0.98), residues: 27 sheet: 1.05 (0.44), residues: 158 loop : -0.32 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.001 0.000 HIS H 110 PHE 0.011 0.001 PHE A 515 TYR 0.010 0.001 TYR L 91 ARG 0.003 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 34 time to evaluate : 0.374 Fit side-chains REVERT: A 357 ARG cc_start: 0.7296 (ttt-90) cc_final: 0.6993 (ttm-80) REVERT: A 462 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6311 (mmtm) REVERT: H 10 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.4695 (mp0) REVERT: H 19 MET cc_start: 0.7197 (ttm) cc_final: 0.6770 (ttp) REVERT: H 97 THR cc_start: 0.9273 (m) cc_final: 0.9015 (p) REVERT: L 5 THR cc_start: 0.7252 (m) cc_final: 0.6575 (t) outliers start: 17 outliers final: 14 residues processed: 50 average time/residue: 0.1524 time to fit residues: 9.6965 Evaluate side-chains 49 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 33 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.7231 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3397 Z= 0.218 Angle : 0.540 9.339 4618 Z= 0.279 Chirality : 0.046 0.217 499 Planarity : 0.003 0.031 586 Dihedral : 5.432 51.294 486 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.63 % Allowed : 23.66 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.42), residues: 416 helix: -2.50 (0.93), residues: 27 sheet: 1.19 (0.44), residues: 151 loop : -0.53 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.001 0.000 HIS H 67 PHE 0.007 0.001 PHE A 392 TYR 0.015 0.001 TYR L 91 ARG 0.003 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 33 time to evaluate : 0.433 Fit side-chains REVERT: A 357 ARG cc_start: 0.7294 (ttt-90) cc_final: 0.7002 (ttm-80) REVERT: A 462 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6427 (mmtt) REVERT: A 468 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7456 (mt) REVERT: H 10 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.4815 (mp0) REVERT: H 19 MET cc_start: 0.7220 (ttm) cc_final: 0.6733 (ttp) outliers start: 20 outliers final: 16 residues processed: 52 average time/residue: 0.1511 time to fit residues: 10.1022 Evaluate side-chains 52 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 33 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.7207 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3397 Z= 0.165 Angle : 0.509 8.814 4618 Z= 0.265 Chirality : 0.045 0.222 499 Planarity : 0.003 0.030 586 Dihedral : 5.317 50.835 486 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.07 % Allowed : 24.51 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.17 (0.42), residues: 416 helix: -1.77 (1.21), residues: 19 sheet: 1.21 (0.44), residues: 151 loop : -0.42 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.001 0.000 HIS H 67 PHE 0.008 0.001 PHE A 515 TYR 0.011 0.001 TYR L 91 ARG 0.002 0.000 ARG A 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 33 time to evaluate : 0.432 Fit side-chains REVERT: A 357 ARG cc_start: 0.7345 (ttt-90) cc_final: 0.7035 (ttm-80) REVERT: A 462 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6310 (mmtm) REVERT: A 468 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7413 (mm) REVERT: H 10 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.4764 (mp0) REVERT: H 19 MET cc_start: 0.7205 (ttm) cc_final: 0.6708 (ttp) REVERT: H 39 GLN cc_start: 0.6869 (OUTLIER) cc_final: 0.6550 (tt0) REVERT: H 97 THR cc_start: 0.9263 (m) cc_final: 0.8983 (p) outliers start: 18 outliers final: 14 residues processed: 50 average time/residue: 0.1240 time to fit residues: 8.1025 Evaluate side-chains 50 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 32 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.164514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.133392 restraints weight = 3558.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.135312 restraints weight = 2896.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.136349 restraints weight = 2549.956| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3397 Z= 0.245 Angle : 0.550 9.828 4618 Z= 0.284 Chirality : 0.046 0.226 499 Planarity : 0.004 0.030 586 Dihedral : 5.452 48.889 486 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.92 % Allowed : 23.66 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.03 (0.42), residues: 416 helix: -1.85 (1.19), residues: 19 sheet: 1.10 (0.44), residues: 151 loop : -0.52 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS H 110 PHE 0.008 0.002 PHE A 347 TYR 0.017 0.001 TYR L 91 ARG 0.002 0.000 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1093.13 seconds wall clock time: 20 minutes 40.28 seconds (1240.28 seconds total)