Starting phenix.real_space_refine on Mon Jun 24 14:52:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv9_38693/06_2024/8xv9_38693_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv9_38693/06_2024/8xv9_38693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv9_38693/06_2024/8xv9_38693.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv9_38693/06_2024/8xv9_38693.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv9_38693/06_2024/8xv9_38693_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv9_38693/06_2024/8xv9_38693_updated.pdb" } resolution = 3.8 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 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 2127 2.51 5 N 472 2.21 5 O 531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 456": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3147 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3110 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'2TA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.76, per 1000 atoms: 0.88 Number of scatterers: 3147 At special positions: 0 Unit cell: (67.41, 70.62, 77.04, 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 531 8.00 N 472 7.00 C 2127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 567.8 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 35 through 39 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 56 through 76 removed outlier: 3.779A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.705A pdb=" N ASP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 98 Processing helix chain 'A' and resid 105 through 129 removed outlier: 3.829A pdb=" N VAL A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 137 through 162 Processing helix chain 'A' and resid 169 through 188 Processing helix chain 'A' and resid 278 through 306 removed outlier: 5.277A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 336 removed outlier: 3.785A pdb=" N TYR A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 348 through 364 Processing helix chain 'A' and resid 369 through 396 removed outlier: 4.016A pdb=" N VAL A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 425 removed outlier: 3.848A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 457 removed outlier: 3.773A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) 201 hydrogen bonds defined for protein. 603 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: 0.77 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 891 1.35 - 1.47: 974 1.47 - 1.59: 1351 1.59 - 1.72: 0 1.72 - 1.84: 30 Bond restraints: 3246 Sorted by residual: bond pdb=" CAQ 2TA A 501 " pdb=" CAR 2TA A 501 " ideal model delta sigma weight residual 1.526 1.343 0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" CAT 2TA A 501 " pdb=" NAP 2TA A 501 " ideal model delta sigma weight residual 1.456 1.285 0.171 2.00e-02 2.50e+03 7.34e+01 bond pdb=" CAQ 2TA A 501 " pdb=" NAP 2TA A 501 " ideal model delta sigma weight residual 1.454 1.583 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" NBE 2TA A 501 " pdb=" SBD 2TA A 501 " ideal model delta sigma weight residual 1.639 1.757 -0.118 2.00e-02 2.50e+03 3.51e+01 bond pdb=" C2 2TA A 501 " pdb=" NAF 2TA A 501 " ideal model delta sigma weight residual 1.361 1.475 -0.114 2.00e-02 2.50e+03 3.26e+01 ... (remaining 3241 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.82: 87 106.82 - 113.61: 1732 113.61 - 120.41: 1364 120.41 - 127.20: 1218 127.20 - 134.00: 36 Bond angle restraints: 4437 Sorted by residual: angle pdb=" C2 2TA A 501 " pdb=" NAF 2TA A 501 " pdb=" CAG 2TA A 501 " ideal model delta sigma weight residual 131.32 114.42 16.90 3.00e+00 1.11e-01 3.17e+01 angle pdb=" C4 2TA A 501 " pdb=" NAW 2TA A 501 " pdb=" CAX 2TA A 501 " ideal model delta sigma weight residual 131.24 120.10 11.14 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA ILE A 36 " pdb=" C ILE A 36 " pdb=" N PRO A 37 " ideal model delta sigma weight residual 118.88 123.77 -4.89 1.54e+00 4.22e-01 1.01e+01 angle pdb=" OBJ 2TA A 501 " pdb=" SBD 2TA A 501 " pdb=" OBK 2TA A 501 " ideal model delta sigma weight residual 118.13 109.12 9.01 3.00e+00 1.11e-01 9.01e+00 angle pdb=" N TYR A 14 " pdb=" CA TYR A 14 " pdb=" C TYR A 14 " ideal model delta sigma weight residual 109.81 115.94 -6.13 2.21e+00 2.05e-01 7.71e+00 ... (remaining 4432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.97: 1801 28.97 - 57.95: 22 57.95 - 86.92: 7 86.92 - 115.90: 2 115.90 - 144.87: 1 Dihedral angle restraints: 1833 sinusoidal: 681 harmonic: 1152 Sorted by residual: dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N TYR A 79 " pdb=" CA TYR A 79 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CAG 2TA A 501 " pdb=" C2 2TA A 501 " pdb=" NAF 2TA A 501 " pdb=" N1 2TA A 501 " ideal model delta sinusoidal sigma weight residual -0.72 -145.59 144.87 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" CA VAL A 425 " pdb=" C VAL A 425 " pdb=" N VAL A 426 " pdb=" CA VAL A 426 " ideal model delta harmonic sigma weight residual -180.00 -158.72 -21.28 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 1830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 292 0.035 - 0.071: 148 0.071 - 0.106: 45 0.106 - 0.141: 13 0.141 - 0.176: 4 Chirality restraints: 502 Sorted by residual: chirality pdb=" CA PHE A 56 " pdb=" N PHE A 56 " pdb=" C PHE A 56 " pdb=" CB PHE A 56 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA TYR A 14 " pdb=" N TYR A 14 " pdb=" C TYR A 14 " pdb=" CB TYR A 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA LYS A 80 " pdb=" N LYS A 80 " pdb=" C LYS A 80 " pdb=" CB LYS A 80 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 499 not shown) Planarity restraints: 529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 373 " 0.018 2.00e-02 2.50e+03 1.64e-02 5.38e+00 pdb=" CG TYR A 373 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 373 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 373 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 373 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 373 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 373 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 373 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 29 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO A 30 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 61 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" C TYR A 61 " 0.034 2.00e-02 2.50e+03 pdb=" O TYR A 61 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 62 " -0.011 2.00e-02 2.50e+03 ... (remaining 526 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1184 2.90 - 3.40: 3079 3.40 - 3.90: 5225 3.90 - 4.40: 5557 4.40 - 4.90: 9626 Nonbonded interactions: 24671 Sorted by model distance: nonbonded pdb=" OE1 GLU A 32 " pdb=" NAW 2TA A 501 " model vdw 2.402 2.520 nonbonded pdb=" OD1 ASP A 75 " pdb=" OH TYR A 79 " model vdw 2.412 2.440 nonbonded pdb=" O PHE A 22 " pdb=" OG SER A 26 " model vdw 2.470 2.440 nonbonded pdb=" OH TYR A 61 " pdb=" OD2 ASP A 427 " model vdw 2.476 2.440 nonbonded pdb=" O LYS A 270 " pdb=" OG SER A 274 " model vdw 2.485 2.440 ... (remaining 24666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.350 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.240 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 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 : 0.008 0.183 3246 Z= 0.433 Angle : 0.936 16.896 4437 Z= 0.449 Chirality : 0.047 0.176 502 Planarity : 0.007 0.051 529 Dihedral : 12.311 144.871 1097 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: -3.53 (0.31), residues: 384 helix: -1.68 (0.22), residues: 279 sheet: None (None), residues: 0 loop : -3.83 (0.44), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 59 HIS 0.003 0.001 HIS A 364 PHE 0.017 0.002 PHE A 439 TYR 0.041 0.002 TYR A 373 ARG 0.001 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.7605 (p) cc_final: 0.7084 (m) REVERT: A 36 ILE cc_start: 0.7864 (tp) cc_final: 0.7439 (tp) REVERT: A 77 VAL cc_start: 0.7653 (m) cc_final: 0.7315 (t) REVERT: A 115 MET cc_start: 0.6896 (ttp) cc_final: 0.6562 (ttp) REVERT: A 152 THR cc_start: 0.7629 (m) cc_final: 0.7115 (p) REVERT: A 306 LYS cc_start: 0.6487 (mmtt) cc_final: 0.6262 (mmtt) REVERT: A 364 HIS cc_start: 0.6529 (t70) cc_final: 0.6234 (t-90) REVERT: A 369 ILE cc_start: 0.8050 (tp) cc_final: 0.7687 (tp) REVERT: A 389 ILE cc_start: 0.7768 (mt) cc_final: 0.7465 (mt) REVERT: A 423 VAL cc_start: 0.7605 (t) cc_final: 0.7056 (m) REVERT: A 440 LEU cc_start: 0.7185 (tp) cc_final: 0.6565 (mt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1216 time to fit residues: 15.1764 Evaluate side-chains 79 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 294 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 HIS ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3246 Z= 0.219 Angle : 0.634 5.880 4437 Z= 0.327 Chirality : 0.042 0.149 502 Planarity : 0.005 0.041 529 Dihedral : 13.592 154.811 440 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.20 % Allowed : 10.81 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.40), residues: 384 helix: 0.43 (0.29), residues: 283 sheet: None (None), residues: 0 loop : -3.05 (0.54), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.024 0.002 PHE A 439 TYR 0.030 0.002 TYR A 126 ARG 0.002 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.8086 (mmp) cc_final: 0.7840 (mmm) REVERT: A 36 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7526 (tp) REVERT: A 77 VAL cc_start: 0.7699 (m) cc_final: 0.7473 (t) REVERT: A 152 THR cc_start: 0.7758 (m) cc_final: 0.7064 (p) REVERT: A 156 VAL cc_start: 0.7971 (t) cc_final: 0.7702 (p) REVERT: A 167 MET cc_start: 0.6070 (mmm) cc_final: 0.5742 (ptp) REVERT: A 369 ILE cc_start: 0.7861 (tp) cc_final: 0.7596 (tp) REVERT: A 386 LEU cc_start: 0.8001 (mt) cc_final: 0.7655 (mm) REVERT: A 389 ILE cc_start: 0.8051 (mt) cc_final: 0.7701 (mt) REVERT: A 423 VAL cc_start: 0.7714 (t) cc_final: 0.7261 (m) outliers start: 4 outliers final: 2 residues processed: 92 average time/residue: 0.1308 time to fit residues: 15.0552 Evaluate side-chains 91 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 272 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN A 310 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3246 Z= 0.246 Angle : 0.635 5.741 4437 Z= 0.331 Chirality : 0.043 0.156 502 Planarity : 0.005 0.043 529 Dihedral : 13.905 162.668 440 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.40 % Allowed : 15.02 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.42), residues: 384 helix: 0.91 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -2.94 (0.56), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 12 HIS 0.004 0.001 HIS A 364 PHE 0.017 0.002 PHE A 439 TYR 0.027 0.002 TYR A 445 ARG 0.005 0.001 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 16 THR cc_start: 0.7670 (m) cc_final: 0.7421 (p) REVERT: A 91 ILE cc_start: 0.7719 (mt) cc_final: 0.7364 (mm) REVERT: A 128 TYR cc_start: 0.6938 (m-80) cc_final: 0.6681 (m-80) REVERT: A 152 THR cc_start: 0.7819 (m) cc_final: 0.7185 (p) REVERT: A 156 VAL cc_start: 0.8002 (t) cc_final: 0.7759 (p) REVERT: A 167 MET cc_start: 0.6528 (mmm) cc_final: 0.6275 (mmm) REVERT: A 363 MET cc_start: 0.6574 (tpt) cc_final: 0.6102 (mtt) REVERT: A 369 ILE cc_start: 0.8052 (tp) cc_final: 0.7851 (tp) REVERT: A 373 TYR cc_start: 0.7759 (m-10) cc_final: 0.7485 (m-80) REVERT: A 423 VAL cc_start: 0.7892 (t) cc_final: 0.7474 (m) REVERT: A 440 LEU cc_start: 0.7322 (tp) cc_final: 0.6773 (mt) outliers start: 8 outliers final: 7 residues processed: 98 average time/residue: 0.1140 time to fit residues: 14.1562 Evaluate side-chains 94 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.0670 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.0010 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.0570 overall best weight: 0.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN A 310 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3246 Z= 0.170 Angle : 0.623 9.793 4437 Z= 0.313 Chirality : 0.039 0.149 502 Planarity : 0.005 0.062 529 Dihedral : 13.973 163.561 440 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.00 % Allowed : 15.62 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.43), residues: 384 helix: 1.11 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -2.70 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 12 HIS 0.002 0.000 HIS A 364 PHE 0.012 0.001 PHE A 112 TYR 0.026 0.002 TYR A 126 ARG 0.002 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.7980 (tmm) cc_final: 0.7251 (tmm) REVERT: A 91 ILE cc_start: 0.7724 (mt) cc_final: 0.7378 (mm) REVERT: A 128 TYR cc_start: 0.6884 (m-80) cc_final: 0.6567 (m-80) REVERT: A 130 VAL cc_start: 0.7885 (p) cc_final: 0.7662 (m) REVERT: A 136 TYR cc_start: 0.6173 (OUTLIER) cc_final: 0.5876 (m-10) REVERT: A 152 THR cc_start: 0.7838 (m) cc_final: 0.7204 (p) REVERT: A 156 VAL cc_start: 0.8001 (t) cc_final: 0.7719 (p) REVERT: A 363 MET cc_start: 0.6680 (tpt) cc_final: 0.6241 (mtt) REVERT: A 369 ILE cc_start: 0.8021 (tp) cc_final: 0.7664 (tp) REVERT: A 373 TYR cc_start: 0.7607 (m-10) cc_final: 0.7355 (m-80) REVERT: A 386 LEU cc_start: 0.7863 (mt) cc_final: 0.7474 (tt) REVERT: A 423 VAL cc_start: 0.7890 (t) cc_final: 0.7450 (m) outliers start: 10 outliers final: 8 residues processed: 94 average time/residue: 0.1288 time to fit residues: 15.0546 Evaluate side-chains 96 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.0070 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN A 310 GLN A 316 ASN A 418 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3246 Z= 0.232 Angle : 0.653 6.802 4437 Z= 0.333 Chirality : 0.041 0.143 502 Planarity : 0.005 0.055 529 Dihedral : 14.026 166.178 440 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.40 % Allowed : 18.62 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.43), residues: 384 helix: 1.16 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -2.38 (0.65), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 12 HIS 0.002 0.001 HIS A 364 PHE 0.015 0.002 PHE A 266 TYR 0.024 0.002 TYR A 445 ARG 0.001 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.8112 (tmm) cc_final: 0.7005 (tmm) REVERT: A 90 PHE cc_start: 0.7537 (m-80) cc_final: 0.7306 (m-80) REVERT: A 91 ILE cc_start: 0.7882 (mt) cc_final: 0.7556 (mm) REVERT: A 128 TYR cc_start: 0.7001 (m-80) cc_final: 0.6760 (m-80) REVERT: A 130 VAL cc_start: 0.7912 (p) cc_final: 0.7640 (m) REVERT: A 152 THR cc_start: 0.7841 (m) cc_final: 0.7190 (p) REVERT: A 156 VAL cc_start: 0.8024 (t) cc_final: 0.7765 (p) REVERT: A 167 MET cc_start: 0.6180 (mmm) cc_final: 0.5651 (ptp) REVERT: A 363 MET cc_start: 0.6690 (tpt) cc_final: 0.6295 (mtt) REVERT: A 373 TYR cc_start: 0.7609 (m-10) cc_final: 0.7383 (m-80) REVERT: A 384 MET cc_start: 0.6915 (tpp) cc_final: 0.6627 (mpp) REVERT: A 386 LEU cc_start: 0.7899 (mt) cc_final: 0.7473 (tt) REVERT: A 423 VAL cc_start: 0.7916 (t) cc_final: 0.7481 (m) REVERT: A 445 TYR cc_start: 0.6392 (t80) cc_final: 0.6051 (t80) outliers start: 8 outliers final: 6 residues processed: 92 average time/residue: 0.1235 time to fit residues: 14.3849 Evaluate side-chains 95 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN A 364 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3246 Z= 0.271 Angle : 0.681 6.866 4437 Z= 0.352 Chirality : 0.042 0.145 502 Planarity : 0.005 0.051 529 Dihedral : 13.931 165.124 440 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.30 % Allowed : 18.62 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.44), residues: 384 helix: 1.13 (0.30), residues: 299 sheet: None (None), residues: 0 loop : -2.21 (0.71), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 94 HIS 0.008 0.002 HIS A 364 PHE 0.021 0.002 PHE A 266 TYR 0.026 0.002 TYR A 126 ARG 0.001 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7854 (mmm) cc_final: 0.7546 (mmm) REVERT: A 28 MET cc_start: 0.8165 (tmm) cc_final: 0.6928 (tmm) REVERT: A 35 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7471 (tp) REVERT: A 91 ILE cc_start: 0.7858 (mt) cc_final: 0.7556 (mm) REVERT: A 95 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6850 (tt) REVERT: A 128 TYR cc_start: 0.7108 (m-80) cc_final: 0.6753 (m-80) REVERT: A 136 TYR cc_start: 0.6139 (OUTLIER) cc_final: 0.5739 (m-10) REVERT: A 152 THR cc_start: 0.7905 (m) cc_final: 0.7273 (p) REVERT: A 156 VAL cc_start: 0.8072 (t) cc_final: 0.7821 (p) REVERT: A 302 LEU cc_start: 0.7929 (tp) cc_final: 0.7634 (tt) REVERT: A 386 LEU cc_start: 0.7832 (mt) cc_final: 0.7346 (tt) REVERT: A 391 VAL cc_start: 0.8575 (t) cc_final: 0.8332 (p) REVERT: A 423 VAL cc_start: 0.7934 (t) cc_final: 0.7492 (m) REVERT: A 445 TYR cc_start: 0.6376 (t80) cc_final: 0.5936 (t80) outliers start: 11 outliers final: 8 residues processed: 94 average time/residue: 0.1093 time to fit residues: 13.2922 Evaluate side-chains 99 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.0670 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3246 Z= 0.226 Angle : 0.661 7.347 4437 Z= 0.335 Chirality : 0.041 0.139 502 Planarity : 0.004 0.045 529 Dihedral : 13.958 168.218 440 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.90 % Allowed : 18.92 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.44), residues: 384 helix: 1.30 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -2.00 (0.70), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.015 0.002 PHE A 266 TYR 0.025 0.002 TYR A 376 ARG 0.001 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8216 (tmm) cc_final: 0.6947 (tmm) REVERT: A 91 ILE cc_start: 0.7855 (mt) cc_final: 0.7555 (mm) REVERT: A 128 TYR cc_start: 0.7140 (m-80) cc_final: 0.6812 (m-80) REVERT: A 136 TYR cc_start: 0.6135 (OUTLIER) cc_final: 0.5749 (m-10) REVERT: A 152 THR cc_start: 0.7900 (m) cc_final: 0.7292 (p) REVERT: A 302 LEU cc_start: 0.7911 (tp) cc_final: 0.7577 (tt) REVERT: A 363 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6184 (mtt) REVERT: A 386 LEU cc_start: 0.7748 (mt) cc_final: 0.7319 (tt) REVERT: A 391 VAL cc_start: 0.8571 (t) cc_final: 0.8329 (p) REVERT: A 423 VAL cc_start: 0.7930 (t) cc_final: 0.7490 (m) REVERT: A 445 TYR cc_start: 0.6348 (t80) cc_final: 0.5968 (t80) outliers start: 13 outliers final: 8 residues processed: 96 average time/residue: 0.1107 time to fit residues: 13.7813 Evaluate side-chains 102 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.0570 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.0370 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3246 Z= 0.212 Angle : 0.661 8.226 4437 Z= 0.331 Chirality : 0.040 0.135 502 Planarity : 0.004 0.040 529 Dihedral : 13.754 159.596 440 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.70 % Allowed : 20.42 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.44), residues: 384 helix: 1.38 (0.30), residues: 297 sheet: None (None), residues: 0 loop : -1.83 (0.71), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.015 0.001 PHE A 266 TYR 0.024 0.002 TYR A 445 ARG 0.001 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.8251 (tmm) cc_final: 0.6958 (tmm) REVERT: A 91 ILE cc_start: 0.7859 (mt) cc_final: 0.7567 (mm) REVERT: A 95 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6920 (tt) REVERT: A 128 TYR cc_start: 0.7159 (m-80) cc_final: 0.6839 (m-80) REVERT: A 136 TYR cc_start: 0.6143 (OUTLIER) cc_final: 0.5703 (m-10) REVERT: A 152 THR cc_start: 0.7890 (m) cc_final: 0.7452 (p) REVERT: A 298 TYR cc_start: 0.6867 (m-10) cc_final: 0.6508 (m-10) REVERT: A 302 LEU cc_start: 0.7780 (tp) cc_final: 0.7456 (tt) REVERT: A 363 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6108 (mtt) REVERT: A 386 LEU cc_start: 0.7793 (mt) cc_final: 0.7371 (tt) REVERT: A 391 VAL cc_start: 0.8568 (t) cc_final: 0.8330 (p) REVERT: A 423 VAL cc_start: 0.7925 (t) cc_final: 0.7484 (m) REVERT: A 445 TYR cc_start: 0.6422 (t80) cc_final: 0.5990 (t80) outliers start: 9 outliers final: 5 residues processed: 94 average time/residue: 0.1172 time to fit residues: 13.8902 Evaluate side-chains 98 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 18 optimal weight: 0.0870 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3246 Z= 0.175 Angle : 0.670 9.485 4437 Z= 0.325 Chirality : 0.039 0.129 502 Planarity : 0.004 0.037 529 Dihedral : 13.505 156.772 440 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.40 % Allowed : 21.62 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.44), residues: 384 helix: 1.63 (0.30), residues: 295 sheet: None (None), residues: 0 loop : -1.86 (0.70), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 59 HIS 0.002 0.001 HIS A 364 PHE 0.014 0.001 PHE A 325 TYR 0.024 0.002 TYR A 445 ARG 0.001 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.8257 (tmm) cc_final: 0.7093 (tmm) REVERT: A 91 ILE cc_start: 0.7792 (mt) cc_final: 0.7497 (mm) REVERT: A 95 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6793 (tt) REVERT: A 117 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8250 (p) REVERT: A 128 TYR cc_start: 0.7144 (m-80) cc_final: 0.6835 (m-80) REVERT: A 130 VAL cc_start: 0.7997 (p) cc_final: 0.7778 (m) REVERT: A 136 TYR cc_start: 0.6153 (OUTLIER) cc_final: 0.5717 (m-10) REVERT: A 152 THR cc_start: 0.7954 (m) cc_final: 0.7483 (p) REVERT: A 302 LEU cc_start: 0.7829 (tp) cc_final: 0.7494 (tt) REVERT: A 363 MET cc_start: 0.6566 (OUTLIER) cc_final: 0.6131 (mtt) REVERT: A 386 LEU cc_start: 0.7805 (mt) cc_final: 0.7373 (tt) REVERT: A 423 VAL cc_start: 0.7896 (t) cc_final: 0.7463 (m) REVERT: A 445 TYR cc_start: 0.6369 (t80) cc_final: 0.6030 (t80) outliers start: 8 outliers final: 4 residues processed: 89 average time/residue: 0.1174 time to fit residues: 13.2892 Evaluate side-chains 94 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.0470 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3246 Z= 0.208 Angle : 0.697 9.468 4437 Z= 0.343 Chirality : 0.041 0.136 502 Planarity : 0.004 0.032 529 Dihedral : 13.346 154.332 440 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.00 % Allowed : 21.62 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.44), residues: 384 helix: 1.58 (0.30), residues: 295 sheet: None (None), residues: 0 loop : -1.78 (0.70), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.021 0.002 PHE A 325 TYR 0.024 0.002 TYR A 445 ARG 0.002 0.000 ARG A 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.8296 (tmm) cc_final: 0.6570 (tmm) REVERT: A 91 ILE cc_start: 0.7858 (mt) cc_final: 0.7561 (mm) REVERT: A 95 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6883 (tt) REVERT: A 117 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8246 (p) REVERT: A 128 TYR cc_start: 0.7218 (m-80) cc_final: 0.6916 (m-80) REVERT: A 136 TYR cc_start: 0.6188 (OUTLIER) cc_final: 0.5746 (m-10) REVERT: A 152 THR cc_start: 0.7936 (m) cc_final: 0.7460 (p) REVERT: A 298 TYR cc_start: 0.6445 (m-10) cc_final: 0.5283 (m-80) REVERT: A 302 LEU cc_start: 0.7832 (tp) cc_final: 0.7506 (tt) REVERT: A 363 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6152 (mtt) REVERT: A 366 THR cc_start: 0.7947 (p) cc_final: 0.7653 (p) REVERT: A 386 LEU cc_start: 0.7772 (mt) cc_final: 0.7327 (tt) REVERT: A 423 VAL cc_start: 0.7903 (t) cc_final: 0.7464 (m) REVERT: A 445 TYR cc_start: 0.6396 (t80) cc_final: 0.5986 (t80) outliers start: 10 outliers final: 6 residues processed: 90 average time/residue: 0.1165 time to fit residues: 13.3035 Evaluate side-chains 96 residues out of total 333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.0070 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.0070 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.155639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.140008 restraints weight = 5456.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.144054 restraints weight = 2905.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.146879 restraints weight = 1792.862| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3246 Z= 0.192 Angle : 0.687 11.459 4437 Z= 0.335 Chirality : 0.041 0.206 502 Planarity : 0.004 0.029 529 Dihedral : 13.283 153.095 440 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.60 % Allowed : 20.72 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.44), residues: 384 helix: 1.62 (0.30), residues: 295 sheet: None (None), residues: 0 loop : -1.79 (0.70), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 59 HIS 0.001 0.000 HIS A 200 PHE 0.014 0.001 PHE A 325 TYR 0.025 0.002 TYR A 126 ARG 0.001 0.000 ARG A 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1142.74 seconds wall clock time: 21 minutes 3.99 seconds (1263.99 seconds total)