Starting phenix.real_space_refine on Tue Mar 11 20:08:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x8y_33060/03_2025/7x8y_33060_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x8y_33060/03_2025/7x8y_33060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x8y_33060/03_2025/7x8y_33060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x8y_33060/03_2025/7x8y_33060.map" model { file = "/net/cci-nas-00/data/ceres_data/7x8y_33060/03_2025/7x8y_33060_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x8y_33060/03_2025/7x8y_33060_trim.cif" } resolution = 4.1 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= 0.002 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: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 2183 2.51 5 N 575 2.21 5 O 662 1.98 5 H 3296 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-5624/modules/chem_data/mon_lib" Total number of atoms: 6731 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3222 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain: "H" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1865 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "L" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1630 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} 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: 3.40, per 1000 atoms: 0.51 Number of scatterers: 6731 At special positions: 0 Unit cell: (61.346, 72.952, 120.205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 O 662 8.00 N 575 7.00 C 2183 6.00 H 3296 1.00 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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 98 " distance=2.04 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 - 3.00 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 695.2 milliseconds 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 802 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 6 sheets defined 9.8% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 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 370 removed outlier: 4.482A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.637A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.166A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 356 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 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 61 through 62 removed outlier: 3.529A pdb=" N ARG H 50 " --> pdb=" O ASP H 61 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.530A pdb=" N SER L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR L 86 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) 87 hydrogen bonds defined for protein. 207 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 3296 1.04 - 1.24: 458 1.24 - 1.44: 1136 1.44 - 1.64: 1910 1.64 - 1.84: 18 Bond restraints: 6818 Sorted by residual: bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N GLN H 1 " pdb=" H GLN H 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" N ASP L 1 " pdb=" H ASP L 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 6813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 11371 1.03 - 2.06: 794 2.06 - 3.08: 44 3.08 - 4.11: 17 4.11 - 5.14: 3 Bond angle restraints: 12229 Sorted by residual: angle pdb=" N GLY H 26 " pdb=" CA GLY H 26 " pdb=" C GLY H 26 " ideal model delta sigma weight residual 114.16 119.30 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" N GLY H 57 " pdb=" CA GLY H 57 " pdb=" C GLY H 57 " ideal model delta sigma weight residual 114.48 111.74 2.74 1.19e+00 7.06e-01 5.31e+00 angle pdb=" CB ARG A 346 " pdb=" CG ARG A 346 " pdb=" CD ARG A 346 " ideal model delta sigma weight residual 111.30 115.18 -3.88 2.30e+00 1.89e-01 2.84e+00 angle pdb=" CG ARG A 346 " pdb=" CD ARG A 346 " pdb=" NE ARG A 346 " ideal model delta sigma weight residual 112.00 115.56 -3.56 2.20e+00 2.07e-01 2.62e+00 angle pdb=" CA GLN H 1 " pdb=" N GLN H 1 " pdb=" H GLN H 1 " ideal model delta sigma weight residual 114.00 109.44 4.56 3.00e+00 1.11e-01 2.31e+00 ... (remaining 12224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 2917 16.28 - 32.56: 282 32.56 - 48.83: 74 48.83 - 65.11: 25 65.11 - 81.39: 7 Dihedral angle restraints: 3305 sinusoidal: 1760 harmonic: 1545 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 20.07 72.93 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CA GLY H 26 " pdb=" C GLY H 26 " pdb=" N PHE H 27 " pdb=" CA PHE H 27 " ideal model delta harmonic sigma weight residual 180.00 157.37 22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA SER H 25 " pdb=" C SER H 25 " pdb=" N GLY H 26 " pdb=" CA GLY H 26 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 3302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 292 0.027 - 0.053: 156 0.053 - 0.080: 35 0.080 - 0.107: 26 0.107 - 0.133: 12 Chirality restraints: 521 Sorted by residual: chirality pdb=" CA VAL H 2 " pdb=" N VAL H 2 " pdb=" C VAL H 2 " pdb=" CB VAL H 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA VAL A 362 " pdb=" N VAL A 362 " pdb=" C VAL A 362 " pdb=" CB VAL A 362 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA VAL L 58 " pdb=" N VAL L 58 " pdb=" C VAL L 58 " pdb=" CB VAL L 58 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 518 not shown) Planarity restraints: 1031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 408 " 0.096 9.50e-02 1.11e+02 3.22e-02 1.24e+00 pdb=" NE ARG A 408 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 408 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 408 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 408 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 408 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 408 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 408 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 408 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 346 " -0.079 9.50e-02 1.11e+02 2.68e-02 1.15e+00 pdb=" NE ARG A 346 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 346 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 346 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 346 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 346 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 346 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 346 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 346 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 112 " 0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO H 113 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO H 113 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO H 113 " 0.014 5.00e-02 4.00e+02 ... (remaining 1028 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 610 2.21 - 2.81: 13812 2.81 - 3.41: 16511 3.41 - 4.00: 21961 4.00 - 4.60: 32493 Nonbonded interactions: 85387 Sorted by model distance: nonbonded pdb=" H LYS A 462 " pdb=" OE2 GLU A 465 " model vdw 1.617 2.450 nonbonded pdb=" OE1 GLN L 55 " pdb=" H GLY L 56 " model vdw 1.631 2.450 nonbonded pdb=" HZ2 LYS A 444 " pdb=" O GLY A 447 " model vdw 1.648 2.450 nonbonded pdb=" O SER H 112 " pdb=" HE1 TRP H 115 " model vdw 1.678 2.450 nonbonded pdb=" OD1 ASN A 422 " pdb=" H ARG A 454 " model vdw 1.694 2.450 ... (remaining 85382 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: 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: 0.120 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.360 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:3.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 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 0.033 3522 Z= 0.174 Angle : 0.529 5.138 4787 Z= 0.283 Chirality : 0.040 0.133 521 Planarity : 0.004 0.042 615 Dihedral : 14.084 81.388 1267 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.09 (0.38), residues: 434 helix: -4.37 (0.55), residues: 26 sheet: -1.42 (0.44), residues: 133 loop : -2.23 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.016 0.001 PHE L 71 TYR 0.013 0.001 TYR L 36 ARG 0.010 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.557 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 LEU cc_start: 0.8460 (pt) cc_final: 0.8244 (pt) REVERT: H 56 ASP cc_start: 0.5517 (t0) cc_final: 0.5221 (t0) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.5425 time to fit residues: 47.2611 Evaluate side-chains 42 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.0270 chunk 32 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.052222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.040296 restraints weight = 71928.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.042373 restraints weight = 31145.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.043761 restraints weight = 17258.996| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3522 Z= 0.194 Angle : 0.518 4.895 4787 Z= 0.280 Chirality : 0.039 0.138 521 Planarity : 0.004 0.037 615 Dihedral : 5.086 42.734 504 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.37), residues: 434 helix: -4.24 (0.48), residues: 32 sheet: -0.97 (0.48), residues: 117 loop : -2.19 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.015 0.001 PHE L 71 TYR 0.006 0.001 TYR A 473 ARG 0.004 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.558 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: symmetry clash REVERT: A 528 LYS cc_start: 0.9673 (mppt) cc_final: 0.9339 (mmtt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.4955 time to fit residues: 30.3179 Evaluate side-chains 34 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 30.0000 chunk 17 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 38 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.050069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.038639 restraints weight = 76959.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040605 restraints weight = 32818.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.041930 restraints weight = 18071.908| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3522 Z= 0.276 Angle : 0.552 5.030 4787 Z= 0.300 Chirality : 0.040 0.137 521 Planarity : 0.004 0.034 615 Dihedral : 4.926 32.423 504 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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: -2.92 (0.38), residues: 434 helix: -4.30 (0.48), residues: 33 sheet: -1.09 (0.47), residues: 122 loop : -2.12 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.029 0.002 PHE A 392 TYR 0.013 0.001 TYR A 508 ARG 0.003 0.001 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.514 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 528 LYS cc_start: 0.9678 (mppt) cc_final: 0.9411 (mmtm) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.4786 time to fit residues: 23.9599 Evaluate side-chains 27 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN H 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.050154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.038644 restraints weight = 74821.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.040637 restraints weight = 31563.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.041989 restraints weight = 17286.115| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3522 Z= 0.184 Angle : 0.505 4.447 4787 Z= 0.270 Chirality : 0.040 0.136 521 Planarity : 0.004 0.035 615 Dihedral : 4.488 22.533 504 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.39), residues: 434 helix: -3.79 (0.66), residues: 31 sheet: -1.17 (0.47), residues: 122 loop : -1.91 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.012 0.001 PHE L 71 TYR 0.011 0.001 TYR L 36 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.530 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: symmetry clash REVERT: A 528 LYS cc_start: 0.9678 (mppt) cc_final: 0.9406 (mmtm) REVERT: L 97 THR cc_start: 0.8335 (m) cc_final: 0.7694 (m) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.4674 time to fit residues: 24.6342 Evaluate side-chains 28 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.049658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.038395 restraints weight = 77300.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.040378 restraints weight = 32678.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.041690 restraints weight = 17884.766| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3522 Z= 0.190 Angle : 0.495 4.694 4787 Z= 0.265 Chirality : 0.039 0.133 521 Planarity : 0.003 0.032 615 Dihedral : 4.300 21.781 504 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.39), residues: 434 helix: -3.10 (0.80), residues: 31 sheet: -1.18 (0.46), residues: 124 loop : -1.88 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.013 0.001 PHE L 71 TYR 0.010 0.001 TYR A 508 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.563 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 528 LYS cc_start: 0.9687 (mppt) cc_final: 0.9422 (mmtm) REVERT: H 56 ASP cc_start: 0.8685 (t0) cc_final: 0.8460 (t0) REVERT: L 97 THR cc_start: 0.8357 (m) cc_final: 0.7779 (m) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.4593 time to fit residues: 24.3714 Evaluate side-chains 29 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** 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 = 0.3324 r_free = 0.3324 target = 0.049525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.038272 restraints weight = 76680.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.040248 restraints weight = 32332.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.041591 restraints weight = 17587.845| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3522 Z= 0.172 Angle : 0.484 4.472 4787 Z= 0.258 Chirality : 0.039 0.135 521 Planarity : 0.003 0.036 615 Dihedral : 4.200 21.917 504 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.39), residues: 434 helix: -2.84 (0.86), residues: 31 sheet: -1.32 (0.46), residues: 123 loop : -1.72 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.010 0.001 PHE L 71 TYR 0.009 0.001 TYR A 508 ARG 0.002 0.000 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.551 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 528 LYS cc_start: 0.9670 (mppt) cc_final: 0.9302 (mmtt) REVERT: H 56 ASP cc_start: 0.8751 (t0) cc_final: 0.8529 (t0) REVERT: L 97 THR cc_start: 0.8317 (m) cc_final: 0.7759 (m) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.4195 time to fit residues: 22.9855 Evaluate side-chains 32 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 30.0000 chunk 2 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 0.0060 chunk 23 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** 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 = 0.3340 r_free = 0.3340 target = 0.050224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.038925 restraints weight = 74752.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.040948 restraints weight = 31223.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.042256 restraints weight = 16955.705| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3522 Z= 0.145 Angle : 0.489 4.683 4787 Z= 0.258 Chirality : 0.040 0.144 521 Planarity : 0.004 0.053 615 Dihedral : 4.122 22.246 504 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.40), residues: 434 helix: -2.87 (0.85), residues: 31 sheet: -1.21 (0.45), residues: 128 loop : -1.71 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP L 35 HIS 0.001 0.000 HIS A 519 PHE 0.009 0.001 PHE L 71 TYR 0.009 0.001 TYR A 508 ARG 0.008 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.538 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 434 ILE cc_start: 0.9607 (mt) cc_final: 0.9309 (tp) REVERT: A 528 LYS cc_start: 0.9664 (mppt) cc_final: 0.9420 (mptt) REVERT: H 56 ASP cc_start: 0.8769 (t0) cc_final: 0.8552 (t0) REVERT: H 102 ASP cc_start: 0.9075 (t0) cc_final: 0.8377 (m-30) REVERT: L 97 THR cc_start: 0.8256 (m) cc_final: 0.7606 (m) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.4507 time to fit residues: 23.5668 Evaluate side-chains 31 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** 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 = 0.3381 r_free = 0.3381 target = 0.050667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.039459 restraints weight = 73776.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.041486 restraints weight = 30771.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.042836 restraints weight = 16617.006| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3522 Z= 0.155 Angle : 0.481 4.311 4787 Z= 0.255 Chirality : 0.040 0.135 521 Planarity : 0.004 0.043 615 Dihedral : 4.046 22.194 504 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.40), residues: 434 helix: -2.63 (1.06), residues: 25 sheet: -1.18 (0.46), residues: 128 loop : -1.55 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.008 0.001 PHE L 71 TYR 0.007 0.001 TYR A 508 ARG 0.009 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.574 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 434 ILE cc_start: 0.9614 (mt) cc_final: 0.9317 (tp) REVERT: A 528 LYS cc_start: 0.9646 (mppt) cc_final: 0.9417 (mptt) REVERT: H 56 ASP cc_start: 0.8681 (t0) cc_final: 0.8469 (t0) REVERT: H 102 ASP cc_start: 0.9093 (t0) cc_final: 0.8385 (m-30) REVERT: L 97 THR cc_start: 0.8314 (m) cc_final: 0.7634 (m) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.4770 time to fit residues: 23.7637 Evaluate side-chains 28 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** 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 = 0.3339 r_free = 0.3339 target = 0.049388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.038479 restraints weight = 78811.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.040411 restraints weight = 33397.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.041705 restraints weight = 18219.987| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3522 Z= 0.203 Angle : 0.503 4.056 4787 Z= 0.272 Chirality : 0.039 0.135 521 Planarity : 0.004 0.045 615 Dihedral : 4.264 21.451 504 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.40), residues: 434 helix: -3.03 (0.93), residues: 25 sheet: -1.12 (0.47), residues: 124 loop : -1.53 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 35 HIS 0.002 0.001 HIS A 519 PHE 0.009 0.001 PHE L 71 TYR 0.009 0.001 TYR A 508 ARG 0.007 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.535 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 434 ILE cc_start: 0.9648 (mt) cc_final: 0.9316 (tp) REVERT: A 528 LYS cc_start: 0.9689 (mppt) cc_final: 0.9428 (mmtm) REVERT: H 56 ASP cc_start: 0.8879 (t0) cc_final: 0.8670 (t0) REVERT: L 97 THR cc_start: 0.8334 (m) cc_final: 0.7744 (m) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.4499 time to fit residues: 21.9791 Evaluate side-chains 28 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** 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 = 0.3325 r_free = 0.3325 target = 0.048861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.038013 restraints weight = 82854.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.039964 restraints weight = 35075.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.041227 restraints weight = 19009.306| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3522 Z= 0.240 Angle : 0.524 3.826 4787 Z= 0.284 Chirality : 0.039 0.135 521 Planarity : 0.004 0.046 615 Dihedral : 4.551 21.376 504 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.40), residues: 434 helix: -2.71 (0.96), residues: 25 sheet: -0.98 (0.47), residues: 128 loop : -1.65 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 35 HIS 0.002 0.001 HIS A 519 PHE 0.011 0.002 PHE L 71 TYR 0.014 0.001 TYR A 508 ARG 0.008 0.001 ARG A 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.517 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: symmetry clash REVERT: A 365 TYR cc_start: 0.9438 (m-10) cc_final: 0.9084 (m-10) REVERT: A 434 ILE cc_start: 0.9662 (mt) cc_final: 0.9339 (tp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.4426 time to fit residues: 20.3702 Evaluate side-chains 28 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 5 optimal weight: 0.2980 chunk 28 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** 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 = 0.3345 r_free = 0.3345 target = 0.049615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.038522 restraints weight = 77786.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.040544 restraints weight = 32898.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.041857 restraints weight = 17769.511| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3522 Z= 0.145 Angle : 0.483 3.815 4787 Z= 0.257 Chirality : 0.040 0.136 521 Planarity : 0.004 0.037 615 Dihedral : 4.262 20.567 504 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.40), residues: 434 helix: -2.28 (1.04), residues: 25 sheet: -1.09 (0.47), residues: 125 loop : -1.50 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.010 0.001 PHE A 392 TYR 0.014 0.001 TYR A 508 ARG 0.007 0.001 ARG A 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2667.62 seconds wall clock time: 46 minutes 17.93 seconds (2777.93 seconds total)