Starting phenix.real_space_refine on Tue Feb 11 03:04:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mkm_23899/02_2025/7mkm_23899.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mkm_23899/02_2025/7mkm_23899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mkm_23899/02_2025/7mkm_23899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mkm_23899/02_2025/7mkm_23899.map" model { file = "/net/cci-nas-00/data/ceres_data/7mkm_23899/02_2025/7mkm_23899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mkm_23899/02_2025/7mkm_23899.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 751 atoms to isotropic. 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 17 5.16 5 C 2030 2.51 5 N 528 2.21 5 O 617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3192 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1500 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 178} Chain: "H" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} 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: 2.72, per 1000 atoms: 0.85 Number of scatterers: 3192 At special positions: 0 Unit cell: (77.72, 67.28, 98.6, 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 17 16.00 O 617 8.00 N 528 7.00 C 2030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " 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 A 601 " - " ASN A 343 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 404.1 milliseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 11.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'L' and resid 48 through 52 removed outlier: 3.810A pdb=" N ASN L 52 " --> pdb=" O ASP L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 4.100A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.734A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 46 through 48 removed outlier: 3.607A pdb=" N GLY H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 37 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN H 39 " --> pdb=" O LYS H 92 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS H 92 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 105 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 3 through 5 removed outlier: 3.771A pdb=" N VAL L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE L 74 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET L 21 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU L 72 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS L 23 " --> pdb=" O TYR L 70 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR L 71 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER L 62 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 47 removed outlier: 4.688A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN L 88 " --> pdb=" O TYR L 33 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR L 35 " --> pdb=" O TYR L 86 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 198 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: 0.70 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1009 1.34 - 1.46: 881 1.46 - 1.58: 1364 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3276 Sorted by residual: bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.426 -0.020 2.00e-02 2.50e+03 1.05e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.65e-01 bond pdb=" CA MET L 77 " pdb=" CB MET L 77 " ideal model delta sigma weight residual 1.513 1.536 -0.023 2.59e-02 1.49e+03 7.75e-01 bond pdb=" C2 NAG A 601 " pdb=" N2 NAG A 601 " ideal model delta sigma weight residual 1.439 1.454 -0.015 2.00e-02 2.50e+03 5.78e-01 ... (remaining 3271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 4317 2.13 - 4.25: 132 4.25 - 6.38: 4 6.38 - 8.50: 2 8.50 - 10.63: 2 Bond angle restraints: 4457 Sorted by residual: angle pdb=" C ARG L 76 " pdb=" N MET L 77 " pdb=" CA MET L 77 " ideal model delta sigma weight residual 122.04 130.76 -8.72 2.11e+00 2.25e-01 1.71e+01 angle pdb=" CA ARG L 60 " pdb=" CB ARG L 60 " pdb=" CG ARG L 60 " ideal model delta sigma weight residual 114.10 121.10 -7.00 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA LEU H 29 " pdb=" CB LEU H 29 " pdb=" CG LEU H 29 " ideal model delta sigma weight residual 116.30 126.93 -10.63 3.50e+00 8.16e-02 9.23e+00 angle pdb=" C LEU H 67 " pdb=" N SER H 68 " pdb=" CA SER H 68 " ideal model delta sigma weight residual 121.62 126.42 -4.80 1.83e+00 2.99e-01 6.87e+00 angle pdb=" C GLY L 65 " pdb=" N CYS L 66 " pdb=" CA CYS L 66 " ideal model delta sigma weight residual 122.59 126.34 -3.75 1.57e+00 4.06e-01 5.70e+00 ... (remaining 4452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 1753 17.71 - 35.41: 159 35.41 - 53.12: 21 53.12 - 70.82: 0 70.82 - 88.53: 2 Dihedral angle restraints: 1935 sinusoidal: 758 harmonic: 1177 Sorted by residual: dihedral pdb=" CA MET L 77 " pdb=" C MET L 77 " pdb=" N GLU L 78 " pdb=" CA GLU L 78 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR H 59 " pdb=" C TYR H 59 " pdb=" N ASN H 60 " pdb=" CA ASN H 60 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ASP L 81 " pdb=" C ASP L 81 " pdb=" N ALA L 82 " pdb=" CA ALA L 82 " ideal model delta harmonic sigma weight residual -180.00 -152.57 -27.43 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 1932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 312 0.037 - 0.074: 113 0.074 - 0.111: 37 0.111 - 0.147: 16 0.147 - 0.184: 2 Chirality restraints: 480 Sorted by residual: chirality pdb=" CB ILE A 402 " pdb=" CA ILE A 402 " pdb=" CG1 ILE A 402 " pdb=" CG2 ILE A 402 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA ILE L 74 " pdb=" N ILE L 74 " pdb=" C ILE L 74 " pdb=" CB ILE L 74 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE L 47 " pdb=" N ILE L 47 " pdb=" C ILE L 47 " pdb=" CB ILE L 47 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 477 not shown) Planarity restraints: 573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO A 491 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.018 2.00e-02 2.50e+03 1.74e-02 3.80e+00 pdb=" CG ASN A 343 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 466 " -0.137 9.50e-02 1.11e+02 6.17e-02 2.96e+00 pdb=" NE ARG A 466 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 466 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 466 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 466 " -0.000 2.00e-02 2.50e+03 ... (remaining 570 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 130 2.72 - 3.27: 3159 3.27 - 3.81: 4603 3.81 - 4.36: 5272 4.36 - 4.90: 9289 Nonbonded interactions: 22453 Sorted by model distance: nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 21 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.274 3.040 nonbonded pdb=" O ASN A 440 " pdb=" ND2 ASN L 91 " model vdw 2.324 3.120 nonbonded pdb=" O ALA A 475 " pdb=" ND2 ASN A 487 " model vdw 2.382 3.120 nonbonded pdb=" OG1 THR A 393 " pdb=" O HIS A 519 " model vdw 2.394 3.040 ... (remaining 22448 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.340 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 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 0.031 3276 Z= 0.171 Angle : 0.795 10.631 4457 Z= 0.432 Chirality : 0.047 0.184 480 Planarity : 0.006 0.062 572 Dihedral : 13.042 88.529 1176 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.38), residues: 400 helix: -3.71 (0.45), residues: 32 sheet: 2.48 (0.49), residues: 100 loop : -2.02 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.002 PHE A 429 TYR 0.018 0.003 TYR L 85 ARG 0.014 0.002 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.354 Fit side-chains REVERT: A 486 PHE cc_start: 0.6384 (t80) cc_final: 0.6143 (t80) REVERT: L 34 TRP cc_start: 0.4286 (m100) cc_final: 0.4080 (m100) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1638 time to fit residues: 11.9466 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.0050 chunk 15 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN L 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.201014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.178168 restraints weight = 5159.939| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 2.97 r_work: 0.4334 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3276 Z= 0.183 Angle : 0.712 8.035 4457 Z= 0.386 Chirality : 0.046 0.253 480 Planarity : 0.005 0.055 572 Dihedral : 7.501 26.191 471 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.15 % Allowed : 10.34 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.39), residues: 400 helix: -2.22 (0.89), residues: 26 sheet: 1.56 (0.45), residues: 113 loop : -1.75 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 436 HIS 0.001 0.001 HIS H 35 PHE 0.029 0.002 PHE A 400 TYR 0.026 0.002 TYR A 423 ARG 0.002 0.000 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.356 Fit side-chains REVERT: A 357 ARG cc_start: 0.7143 (ttt-90) cc_final: 0.6924 (ttt-90) REVERT: A 365 TYR cc_start: 0.6367 (m-80) cc_final: 0.5708 (m-80) REVERT: A 410 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7921 (mm) REVERT: A 465 GLU cc_start: 0.6826 (tp30) cc_final: 0.6393 (tp30) REVERT: A 466 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7325 (mtm-85) REVERT: A 486 PHE cc_start: 0.7041 (t80) cc_final: 0.6547 (t80) outliers start: 4 outliers final: 2 residues processed: 56 average time/residue: 0.1676 time to fit residues: 11.3104 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 22 optimal weight: 0.0770 chunk 34 optimal weight: 0.5980 chunk 30 optimal weight: 0.0030 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.3548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.199745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.176863 restraints weight = 5035.221| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 2.99 r_work: 0.4307 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3276 Z= 0.181 Angle : 0.670 8.402 4457 Z= 0.363 Chirality : 0.045 0.283 480 Planarity : 0.005 0.052 572 Dihedral : 6.862 27.503 471 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.30 % Allowed : 12.07 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.39), residues: 400 helix: -1.76 (1.04), residues: 26 sheet: 1.20 (0.45), residues: 115 loop : -1.69 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 36 HIS 0.001 0.000 HIS A 519 PHE 0.013 0.002 PHE A 400 TYR 0.012 0.001 TYR A 451 ARG 0.002 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.328 Fit side-chains REVERT: A 357 ARG cc_start: 0.7317 (ttt-90) cc_final: 0.7037 (ttt-90) REVERT: A 365 TYR cc_start: 0.6447 (m-80) cc_final: 0.5759 (m-80) REVERT: A 410 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7924 (mm) REVERT: A 465 GLU cc_start: 0.7158 (tp30) cc_final: 0.6766 (tp30) REVERT: A 486 PHE cc_start: 0.6985 (t80) cc_final: 0.6531 (t80) REVERT: H 82 MET cc_start: -0.1176 (tpp) cc_final: -0.1535 (tpt) outliers start: 8 outliers final: 3 residues processed: 58 average time/residue: 0.1649 time to fit residues: 11.6711 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain L residue 32 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 0.0270 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.0870 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.195563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.174057 restraints weight = 5103.461| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 2.76 r_work: 0.4292 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3276 Z= 0.180 Angle : 0.655 8.413 4457 Z= 0.355 Chirality : 0.045 0.260 480 Planarity : 0.005 0.050 572 Dihedral : 6.529 27.156 471 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.01 % Allowed : 12.93 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.39), residues: 400 helix: -1.73 (1.03), residues: 26 sheet: 0.88 (0.45), residues: 110 loop : -1.75 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 47 HIS 0.001 0.001 HIS H 35 PHE 0.011 0.002 PHE A 400 TYR 0.011 0.002 TYR A 451 ARG 0.002 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.308 Fit side-chains REVERT: A 357 ARG cc_start: 0.7256 (ttt-90) cc_final: 0.6984 (ttt-90) REVERT: A 410 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7989 (mm) REVERT: A 465 GLU cc_start: 0.7066 (tp30) cc_final: 0.6754 (tp30) REVERT: A 486 PHE cc_start: 0.6783 (t80) cc_final: 0.6436 (t80) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 0.1714 time to fit residues: 11.3056 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain L residue 32 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 0.0000 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 0.0770 chunk 19 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.196651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.174862 restraints weight = 5269.453| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 2.71 r_work: 0.4319 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3276 Z= 0.149 Angle : 0.614 8.198 4457 Z= 0.332 Chirality : 0.044 0.209 480 Planarity : 0.004 0.048 572 Dihedral : 6.087 26.868 471 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.30 % Allowed : 14.08 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.39), residues: 400 helix: -1.66 (1.04), residues: 26 sheet: 0.62 (0.48), residues: 104 loop : -1.73 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 36 HIS 0.001 0.000 HIS H 35 PHE 0.011 0.001 PHE A 400 TYR 0.008 0.001 TYR A 453 ARG 0.001 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.303 Fit side-chains REVERT: A 357 ARG cc_start: 0.7197 (ttt-90) cc_final: 0.6930 (ttt-90) REVERT: A 410 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7850 (mm) REVERT: A 465 GLU cc_start: 0.6985 (tp30) cc_final: 0.6739 (tp30) REVERT: A 486 PHE cc_start: 0.6779 (t80) cc_final: 0.6468 (t80) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.1641 time to fit residues: 10.1515 Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.0070 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.191914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.170295 restraints weight = 5424.149| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 2.71 r_work: 0.4266 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3276 Z= 0.243 Angle : 0.687 8.584 4457 Z= 0.373 Chirality : 0.046 0.260 480 Planarity : 0.005 0.050 572 Dihedral : 6.452 26.817 471 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.01 % Allowed : 15.23 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.39), residues: 400 helix: -2.06 (1.00), residues: 27 sheet: 0.06 (0.45), residues: 115 loop : -1.73 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 36 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.002 PHE A 497 TYR 0.017 0.002 TYR H 58 ARG 0.003 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.327 Fit side-chains REVERT: A 357 ARG cc_start: 0.7352 (ttt-90) cc_final: 0.7129 (ttt-90) REVERT: A 410 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7957 (mm) REVERT: A 417 LYS cc_start: 0.5784 (mmtt) cc_final: 0.5564 (mmtt) REVERT: A 465 GLU cc_start: 0.7039 (tp30) cc_final: 0.6781 (tp30) REVERT: A 466 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7332 (mtm-85) REVERT: A 486 PHE cc_start: 0.6754 (t80) cc_final: 0.6435 (t80) outliers start: 7 outliers final: 4 residues processed: 55 average time/residue: 0.1700 time to fit residues: 11.3265 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN L 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.190433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.168901 restraints weight = 5162.078| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 2.81 r_work: 0.4236 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3276 Z= 0.254 Angle : 0.711 8.193 4457 Z= 0.385 Chirality : 0.046 0.261 480 Planarity : 0.005 0.052 572 Dihedral : 6.612 27.447 471 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.30 % Allowed : 14.66 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.09 (0.39), residues: 400 helix: -2.14 (1.00), residues: 27 sheet: -0.06 (0.47), residues: 110 loop : -2.02 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP H 36 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.002 PHE A 497 TYR 0.018 0.002 TYR H 58 ARG 0.003 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.277 Fit side-chains REVERT: A 357 ARG cc_start: 0.7395 (ttt-90) cc_final: 0.7160 (ttt-90) REVERT: A 410 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7994 (mm) REVERT: A 417 LYS cc_start: 0.5769 (mmtt) cc_final: 0.5558 (mmtm) REVERT: A 465 GLU cc_start: 0.7066 (tp30) cc_final: 0.6853 (tp30) REVERT: A 466 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7432 (mtm-85) REVERT: A 486 PHE cc_start: 0.6695 (t80) cc_final: 0.6388 (t80) REVERT: A 509 ARG cc_start: 0.7051 (mtt180) cc_final: 0.6058 (mtp85) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.2034 time to fit residues: 13.1375 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.0670 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- 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 = 0.4580 r_free = 0.4580 target = 0.192470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.170926 restraints weight = 5146.475| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 2.84 r_work: 0.4264 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3276 Z= 0.183 Angle : 0.680 8.077 4457 Z= 0.364 Chirality : 0.045 0.215 480 Planarity : 0.005 0.053 572 Dihedral : 6.194 26.795 471 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.72 % Allowed : 16.38 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.10 (0.39), residues: 400 helix: -2.24 (0.86), residues: 33 sheet: 0.12 (0.50), residues: 100 loop : -2.02 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 36 HIS 0.001 0.001 HIS H 35 PHE 0.013 0.001 PHE A 400 TYR 0.021 0.002 TYR L 35 ARG 0.004 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.425 Fit side-chains REVERT: A 357 ARG cc_start: 0.7379 (ttt-90) cc_final: 0.7143 (ttt-90) REVERT: A 410 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7963 (mm) REVERT: A 417 LYS cc_start: 0.5765 (mmtt) cc_final: 0.5551 (mmtt) REVERT: A 466 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7413 (mtm-85) REVERT: A 486 PHE cc_start: 0.6634 (t80) cc_final: 0.6359 (t80) REVERT: A 509 ARG cc_start: 0.6929 (mtt180) cc_final: 0.5961 (mtp180) REVERT: H 103 ASP cc_start: 0.7675 (t0) cc_final: 0.7309 (m-30) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.1865 time to fit residues: 11.0600 Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 0.0070 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.0370 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.2876 ------------------------------------------------------------------------------- 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 = 0.4596 r_free = 0.4596 target = 0.193888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.172158 restraints weight = 5129.703| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 2.87 r_work: 0.4276 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3276 Z= 0.173 Angle : 0.674 8.051 4457 Z= 0.360 Chirality : 0.044 0.192 480 Planarity : 0.005 0.052 572 Dihedral : 5.891 25.828 471 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.72 % Allowed : 16.38 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.06 (0.40), residues: 400 helix: -2.24 (0.87), residues: 33 sheet: -0.05 (0.50), residues: 102 loop : -1.91 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 36 HIS 0.001 0.000 HIS H 35 PHE 0.011 0.001 PHE A 400 TYR 0.015 0.001 TYR L 35 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.324 Fit side-chains REVERT: A 357 ARG cc_start: 0.7359 (ttt-90) cc_final: 0.7111 (ttt-90) REVERT: A 410 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7924 (mm) REVERT: A 417 LYS cc_start: 0.5688 (mmtt) cc_final: 0.5372 (mmtt) REVERT: A 466 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7633 (mtm-85) REVERT: A 486 PHE cc_start: 0.6612 (t80) cc_final: 0.6378 (t80) REVERT: A 509 ARG cc_start: 0.6981 (mtt180) cc_final: 0.6022 (mtp180) REVERT: H 103 ASP cc_start: 0.7685 (t0) cc_final: 0.7356 (m-30) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.1800 time to fit residues: 11.2444 Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.190474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.168885 restraints weight = 5105.603| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 2.86 r_work: 0.4235 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3276 Z= 0.248 Angle : 0.730 8.724 4457 Z= 0.393 Chirality : 0.046 0.213 480 Planarity : 0.005 0.055 572 Dihedral : 6.293 25.858 471 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.72 % Allowed : 17.24 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.27 (0.40), residues: 400 helix: -2.37 (0.85), residues: 33 sheet: -0.29 (0.53), residues: 97 loop : -1.98 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 436 HIS 0.001 0.001 HIS H 35 PHE 0.011 0.002 PHE A 497 TYR 0.021 0.002 TYR L 35 ARG 0.004 0.001 ARG L 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.304 Fit side-chains REVERT: A 357 ARG cc_start: 0.7439 (ttt-90) cc_final: 0.7208 (ttt-90) REVERT: A 410 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8070 (mm) REVERT: A 417 LYS cc_start: 0.5658 (mmtt) cc_final: 0.5446 (mmtm) REVERT: A 466 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.7606 (mtm-85) REVERT: A 486 PHE cc_start: 0.6646 (t80) cc_final: 0.6357 (t80) REVERT: A 509 ARG cc_start: 0.7091 (mtt180) cc_final: 0.6122 (mtp180) REVERT: H 103 ASP cc_start: 0.7707 (t0) cc_final: 0.7352 (m-30) outliers start: 6 outliers final: 5 residues processed: 51 average time/residue: 0.2081 time to fit residues: 12.4821 Evaluate side-chains 51 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.0000 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 overall best weight: 0.3184 ------------------------------------------------------------------------------- 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 = 0.4580 r_free = 0.4580 target = 0.192549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.171032 restraints weight = 5161.667| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.85 r_work: 0.4262 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3276 Z= 0.181 Angle : 0.687 8.197 4457 Z= 0.368 Chirality : 0.045 0.171 480 Planarity : 0.005 0.053 572 Dihedral : 6.037 26.024 471 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.72 % Allowed : 16.95 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.12 (0.41), residues: 400 helix: -2.30 (0.86), residues: 33 sheet: -0.12 (0.51), residues: 105 loop : -1.95 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 36 HIS 0.001 0.000 HIS H 35 PHE 0.012 0.001 PHE A 400 TYR 0.017 0.002 TYR L 35 ARG 0.003 0.001 ARG A 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2028.35 seconds wall clock time: 36 minutes 46.84 seconds (2206.84 seconds total)