Starting phenix.real_space_refine on Wed Mar 5 17:27:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7w_39830/03_2025/8z7w_39830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7w_39830/03_2025/8z7w_39830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7w_39830/03_2025/8z7w_39830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7w_39830/03_2025/8z7w_39830.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7w_39830/03_2025/8z7w_39830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7w_39830/03_2025/8z7w_39830.cif" } resolution = 3.09 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= 0.103 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 15 5.16 5 C 2095 2.51 5 N 468 2.21 5 O 529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3107 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3098 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.61, per 1000 atoms: 0.84 Number of scatterers: 3107 At special positions: 0 Unit cell: (64, 68, 71, 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 15 16.00 O 529 8.00 N 468 7.00 C 2095 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 379.5 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 87.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 32 through 36 removed outlier: 3.553A pdb=" N LEU A 35 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE A 36 " --> pdb=" O PRO A 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 32 through 36' Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.729A pdb=" N SER A 40 " --> pdb=" O PRO A 37 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 41 " --> pdb=" O TYR A 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 37 through 41' Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.626A pdb=" N THR A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 53' Processing helix chain 'A' and resid 55 through 73 removed outlier: 4.019A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.864A pdb=" N VAL A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 99 removed outlier: 3.590A pdb=" N ILE A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 131 removed outlier: 3.502A pdb=" N MET A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 164 Processing helix chain 'A' and resid 168 through 189 Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 280 through 307 removed outlier: 4.286A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 337 removed outlier: 4.446A pdb=" N GLY A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 366 removed outlier: 3.720A pdb=" N LEU A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLU A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 398 Processing helix chain 'A' and resid 402 through 426 Processing helix chain 'A' and resid 434 through 461 removed outlier: 3.913A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 720 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: 0.80 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 449 1.30 - 1.43: 966 1.43 - 1.56: 1758 1.56 - 1.69: 0 1.69 - 1.82: 26 Bond restraints: 3199 Sorted by residual: bond pdb=" C ALA A 447 " pdb=" O ALA A 447 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.18e-02 7.18e+03 3.75e+01 bond pdb=" C ALA A 450 " pdb=" O ALA A 450 " ideal model delta sigma weight residual 1.237 1.166 0.071 1.17e-02 7.31e+03 3.66e+01 bond pdb=" C PRO A 69 " pdb=" O PRO A 69 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.30e-02 5.92e+03 2.18e+01 bond pdb=" C ALA A 321 " pdb=" O ALA A 321 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.22e-02 6.72e+03 2.14e+01 bond pdb=" C TYR A 315 " pdb=" O TYR A 315 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.17e-02 7.31e+03 1.72e+01 ... (remaining 3194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 4159 2.21 - 4.41: 173 4.41 - 6.62: 29 6.62 - 8.83: 6 8.83 - 11.04: 5 Bond angle restraints: 4372 Sorted by residual: angle pdb=" N LEU A 35 " pdb=" CA LEU A 35 " pdb=" C LEU A 35 " ideal model delta sigma weight residual 112.04 102.68 9.36 1.44e+00 4.82e-01 4.23e+01 angle pdb=" N ALA A 447 " pdb=" CA ALA A 447 " pdb=" C ALA A 447 " ideal model delta sigma weight residual 111.33 104.22 7.11 1.21e+00 6.83e-01 3.46e+01 angle pdb=" CB GLU A 320 " pdb=" CG GLU A 320 " pdb=" CD GLU A 320 " ideal model delta sigma weight residual 112.60 122.33 -9.73 1.70e+00 3.46e-01 3.27e+01 angle pdb=" C ASN A 45 " pdb=" CA ASN A 45 " pdb=" CB ASN A 45 " ideal model delta sigma weight residual 111.80 119.94 -8.14 1.46e+00 4.69e-01 3.11e+01 angle pdb=" C THR A 47 " pdb=" CA THR A 47 " pdb=" CB THR A 47 " ideal model delta sigma weight residual 109.76 120.80 -11.04 1.99e+00 2.53e-01 3.08e+01 ... (remaining 4367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 1504 16.33 - 32.67: 222 32.67 - 49.00: 59 49.00 - 65.33: 20 65.33 - 81.66: 3 Dihedral angle restraints: 1808 sinusoidal: 659 harmonic: 1149 Sorted by residual: dihedral pdb=" C ASN A 45 " pdb=" N ASN A 45 " pdb=" CA ASN A 45 " pdb=" CB ASN A 45 " ideal model delta harmonic sigma weight residual -122.60 -142.73 20.13 0 2.50e+00 1.60e-01 6.48e+01 dihedral pdb=" N ASN A 45 " pdb=" C ASN A 45 " pdb=" CA ASN A 45 " pdb=" CB ASN A 45 " ideal model delta harmonic sigma weight residual 122.80 141.30 -18.50 0 2.50e+00 1.60e-01 5.48e+01 dihedral pdb=" C THR A 47 " pdb=" N THR A 47 " pdb=" CA THR A 47 " pdb=" CB THR A 47 " ideal model delta harmonic sigma weight residual -122.00 -133.88 11.88 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 1805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 484 0.151 - 0.301: 18 0.301 - 0.452: 2 0.452 - 0.603: 0 0.603 - 0.753: 1 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA ASN A 45 " pdb=" N ASN A 45 " pdb=" C ASN A 45 " pdb=" CB ASN A 45 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA LEU A 46 " pdb=" N LEU A 46 " pdb=" C LEU A 46 " pdb=" CB LEU A 46 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ILE A 449 " pdb=" N ILE A 449 " pdb=" C ILE A 449 " pdb=" CB ILE A 449 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 502 not shown) Planarity restraints: 524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 501 " -0.438 2.00e-02 2.50e+03 3.18e-01 2.27e+03 pdb=" C03 MF8 A 501 " 0.491 2.00e-02 2.50e+03 pdb=" C04 MF8 A 501 " -0.007 2.00e-02 2.50e+03 pdb=" C07 MF8 A 501 " -0.015 2.00e-02 2.50e+03 pdb=" N02 MF8 A 501 " 0.013 2.00e-02 2.50e+03 pdb=" N05 MF8 A 501 " -0.000 2.00e-02 2.50e+03 pdb=" N06 MF8 A 501 " -0.032 2.00e-02 2.50e+03 pdb=" N08 MF8 A 501 " -0.492 2.00e-02 2.50e+03 pdb=" N09 MF8 A 501 " 0.481 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 69 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PRO A 69 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO A 69 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 70 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 70 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C VAL A 70 " -0.048 2.00e-02 2.50e+03 pdb=" O VAL A 70 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE A 71 " 0.017 2.00e-02 2.50e+03 ... (remaining 521 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 699 2.77 - 3.30: 3279 3.30 - 3.84: 5570 3.84 - 4.37: 6550 4.37 - 4.90: 11132 Nonbonded interactions: 27230 Sorted by model distance: nonbonded pdb=" OD1 ASP A 75 " pdb=" OH TYR A 79 " model vdw 2.241 3.040 nonbonded pdb=" OE1 GLN A 294 " pdb=" OH TYR A 442 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR A 128 " pdb=" OG SER A 140 " model vdw 2.257 3.040 nonbonded pdb=" O PHE A 287 " pdb=" OH TYR A 445 " model vdw 2.319 3.040 nonbonded pdb=" OH TYR A 126 " pdb=" O PRO A 191 " model vdw 2.325 3.040 ... (remaining 27225 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 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.620 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 : 0.007 0.072 3199 Z= 0.467 Angle : 1.027 11.035 4372 Z= 0.687 Chirality : 0.070 0.753 505 Planarity : 0.015 0.318 524 Dihedral : 17.007 81.664 1074 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.30 % Allowed : 25.83 % Favored : 70.87 % Cbeta Deviations : 0.82 % 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: -0.06 (0.43), residues: 383 helix: 0.09 (0.28), residues: 318 sheet: None (None), residues: 0 loop : 0.09 (0.88), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.031 0.002 PHE A 279 TYR 0.017 0.002 TYR A 459 ARG 0.003 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.314 Fit side-chains REVERT: A 280 TYR cc_start: 0.8306 (t80) cc_final: 0.7886 (t80) REVERT: A 340 ASN cc_start: 0.8034 (p0) cc_final: 0.7305 (t0) outliers start: 11 outliers final: 4 residues processed: 52 average time/residue: 0.1644 time to fit residues: 10.4829 Evaluate side-chains 45 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 454 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.133609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.113910 restraints weight = 3746.906| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.58 r_work: 0.3124 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3199 Z= 0.279 Angle : 0.666 8.978 4372 Z= 0.348 Chirality : 0.044 0.219 505 Planarity : 0.005 0.033 524 Dihedral : 5.067 31.535 429 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.00 % Allowed : 25.53 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.43), residues: 383 helix: 0.96 (0.29), residues: 325 sheet: None (None), residues: 0 loop : 0.44 (0.89), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.004 0.001 HIS A 364 PHE 0.023 0.002 PHE A 71 TYR 0.014 0.002 TYR A 280 ARG 0.001 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.348 Fit side-chains REVERT: A 120 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6409 (pt0) REVERT: A 146 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8370 (t) REVERT: A 265 TRP cc_start: 0.7973 (t60) cc_final: 0.7616 (t60) REVERT: A 315 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.6907 (t80) REVERT: A 340 ASN cc_start: 0.8171 (p0) cc_final: 0.7121 (t0) REVERT: A 385 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8151 (tp) outliers start: 10 outliers final: 3 residues processed: 57 average time/residue: 0.1181 time to fit residues: 8.9531 Evaluate side-chains 49 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.0270 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.151808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131239 restraints weight = 3483.909| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.67 r_work: 0.3403 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3199 Z= 0.250 Angle : 0.618 10.112 4372 Z= 0.318 Chirality : 0.042 0.217 505 Planarity : 0.004 0.035 524 Dihedral : 4.351 19.645 423 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.50 % Allowed : 24.32 % Favored : 71.17 % 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: 1.43 (0.43), residues: 383 helix: 1.13 (0.28), residues: 327 sheet: None (None), residues: 0 loop : 0.37 (0.91), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.017 0.001 PHE A 71 TYR 0.013 0.002 TYR A 298 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.324 Fit side-chains REVERT: A 120 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6783 (pt0) REVERT: A 146 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8452 (t) REVERT: A 265 TRP cc_start: 0.8274 (t60) cc_final: 0.7917 (t60) REVERT: A 280 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.6473 (m-80) REVERT: A 315 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7014 (t80) REVERT: A 340 ASN cc_start: 0.8339 (p0) cc_final: 0.7227 (t0) REVERT: A 385 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8276 (tp) outliers start: 15 outliers final: 8 residues processed: 53 average time/residue: 0.1097 time to fit residues: 7.7069 Evaluate side-chains 54 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.152559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131830 restraints weight = 3553.905| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.69 r_work: 0.3392 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3199 Z= 0.232 Angle : 0.597 9.880 4372 Z= 0.308 Chirality : 0.042 0.211 505 Planarity : 0.004 0.034 524 Dihedral : 4.295 19.855 423 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 6.01 % Allowed : 22.82 % Favored : 71.17 % 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: 1.57 (0.43), residues: 383 helix: 1.24 (0.29), residues: 324 sheet: None (None), residues: 0 loop : 0.34 (0.91), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.001 PHE A 71 TYR 0.013 0.001 TYR A 38 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6780 (pt0) REVERT: A 146 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8499 (t) REVERT: A 265 TRP cc_start: 0.8360 (t60) cc_final: 0.8048 (t60) REVERT: A 280 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.6568 (m-80) REVERT: A 336 TYR cc_start: 0.8514 (t80) cc_final: 0.8311 (t80) REVERT: A 340 ASN cc_start: 0.8365 (p0) cc_final: 0.7310 (t0) REVERT: A 385 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8292 (tp) REVERT: A 438 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6988 (tt0) outliers start: 20 outliers final: 9 residues processed: 58 average time/residue: 0.1203 time to fit residues: 9.3624 Evaluate side-chains 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.148923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128279 restraints weight = 3558.317| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.69 r_work: 0.3387 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3199 Z= 0.247 Angle : 0.596 9.968 4372 Z= 0.306 Chirality : 0.043 0.213 505 Planarity : 0.004 0.035 524 Dihedral : 4.302 20.182 423 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.41 % Allowed : 21.32 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.43), residues: 383 helix: 1.25 (0.29), residues: 323 sheet: None (None), residues: 0 loop : 0.17 (0.90), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.001 PHE A 71 TYR 0.015 0.002 TYR A 298 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6979 (pt0) REVERT: A 146 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8506 (t) REVERT: A 265 TRP cc_start: 0.8408 (t60) cc_final: 0.8145 (t60) REVERT: A 280 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.6544 (m-80) REVERT: A 336 TYR cc_start: 0.8615 (t80) cc_final: 0.8374 (t80) REVERT: A 340 ASN cc_start: 0.8300 (p0) cc_final: 0.7293 (t0) REVERT: A 385 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8280 (tp) outliers start: 18 outliers final: 11 residues processed: 57 average time/residue: 0.1298 time to fit residues: 9.9973 Evaluate side-chains 54 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 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 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.151705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.131015 restraints weight = 3582.658| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.69 r_work: 0.3393 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3199 Z= 0.242 Angle : 0.592 9.908 4372 Z= 0.303 Chirality : 0.042 0.212 505 Planarity : 0.004 0.036 524 Dihedral : 4.266 20.202 423 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 6.01 % Allowed : 19.82 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.43), residues: 383 helix: 1.26 (0.29), residues: 322 sheet: None (None), residues: 0 loop : 0.04 (0.86), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.001 PHE A 71 TYR 0.014 0.001 TYR A 298 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6945 (pt0) REVERT: A 146 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8512 (t) REVERT: A 265 TRP cc_start: 0.8446 (t60) cc_final: 0.8203 (t60) REVERT: A 280 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.6564 (m-80) REVERT: A 340 ASN cc_start: 0.8349 (p0) cc_final: 0.7241 (t0) REVERT: A 385 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8276 (tp) outliers start: 20 outliers final: 11 residues processed: 53 average time/residue: 0.1142 time to fit residues: 8.2160 Evaluate side-chains 54 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.152519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.132095 restraints weight = 3465.017| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.65 r_work: 0.3411 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3199 Z= 0.228 Angle : 0.584 10.034 4372 Z= 0.299 Chirality : 0.042 0.210 505 Planarity : 0.004 0.036 524 Dihedral : 4.233 20.392 423 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.80 % Allowed : 20.42 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.43), residues: 383 helix: 1.35 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.06 (0.84), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.014 0.001 PHE A 71 TYR 0.012 0.001 TYR A 298 ARG 0.001 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7036 (pt0) REVERT: A 265 TRP cc_start: 0.8443 (t60) cc_final: 0.8202 (t60) REVERT: A 280 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.6581 (m-80) REVERT: A 340 ASN cc_start: 0.8355 (p0) cc_final: 0.7238 (t0) REVERT: A 385 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8259 (tp) outliers start: 16 outliers final: 11 residues processed: 53 average time/residue: 0.1070 time to fit residues: 7.5680 Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.0270 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.153432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132953 restraints weight = 3491.150| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.66 r_work: 0.3422 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3199 Z= 0.209 Angle : 0.575 10.041 4372 Z= 0.293 Chirality : 0.041 0.208 505 Planarity : 0.004 0.036 524 Dihedral : 4.180 20.342 423 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.50 % Allowed : 21.02 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.43), residues: 383 helix: 1.38 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.17 (0.85), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.014 0.001 PHE A 71 TYR 0.014 0.001 TYR A 298 ARG 0.000 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7031 (pt0) REVERT: A 146 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8480 (t) REVERT: A 265 TRP cc_start: 0.8433 (t60) cc_final: 0.8193 (t60) REVERT: A 280 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.6561 (m-80) REVERT: A 340 ASN cc_start: 0.8339 (p0) cc_final: 0.7234 (t0) REVERT: A 385 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8267 (tp) outliers start: 15 outliers final: 10 residues processed: 52 average time/residue: 0.1091 time to fit residues: 7.5816 Evaluate side-chains 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.152558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132176 restraints weight = 3526.457| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.67 r_work: 0.3411 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3199 Z= 0.229 Angle : 0.584 10.055 4372 Z= 0.298 Chirality : 0.042 0.208 505 Planarity : 0.004 0.036 524 Dihedral : 4.215 20.350 423 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.50 % Allowed : 21.92 % Favored : 73.57 % 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: 1.68 (0.43), residues: 383 helix: 1.36 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.13 (0.84), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.001 PHE A 71 TYR 0.017 0.001 TYR A 383 ARG 0.000 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7131 (pt0) REVERT: A 146 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8494 (t) REVERT: A 265 TRP cc_start: 0.8442 (t60) cc_final: 0.8176 (t60) REVERT: A 280 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.6568 (m-80) REVERT: A 340 ASN cc_start: 0.8351 (p0) cc_final: 0.7246 (t0) REVERT: A 385 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8274 (tp) outliers start: 15 outliers final: 11 residues processed: 53 average time/residue: 0.1118 time to fit residues: 7.9395 Evaluate side-chains 59 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.151688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131512 restraints weight = 3450.953| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.62 r_work: 0.3409 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3199 Z= 0.242 Angle : 0.594 10.125 4372 Z= 0.302 Chirality : 0.042 0.212 505 Planarity : 0.004 0.038 524 Dihedral : 4.241 20.283 423 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.20 % Allowed : 22.52 % Favored : 73.27 % 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: 1.65 (0.43), residues: 383 helix: 1.35 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.11 (0.83), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.001 PHE A 71 TYR 0.017 0.002 TYR A 383 ARG 0.001 0.000 ARG A 429 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.8440 (tmm) cc_final: 0.7985 (tmm) REVERT: A 120 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7165 (pt0) REVERT: A 146 VAL cc_start: 0.8782 (OUTLIER) cc_final: 0.8508 (t) REVERT: A 280 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.6592 (m-80) REVERT: A 340 ASN cc_start: 0.8349 (p0) cc_final: 0.7249 (t0) REVERT: A 385 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8293 (tp) REVERT: A 452 ILE cc_start: 0.7487 (mt) cc_final: 0.7137 (mt) outliers start: 14 outliers final: 10 residues processed: 55 average time/residue: 0.1178 time to fit residues: 8.7442 Evaluate side-chains 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.149568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129964 restraints weight = 3532.925| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.58 r_work: 0.3416 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3199 Z= 0.213 Angle : 0.582 10.034 4372 Z= 0.297 Chirality : 0.041 0.206 505 Planarity : 0.004 0.038 524 Dihedral : 4.227 20.406 423 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.50 % Allowed : 22.22 % Favored : 73.27 % 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: 1.75 (0.43), residues: 383 helix: 1.39 (0.28), residues: 322 sheet: None (None), residues: 0 loop : 0.31 (0.83), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.014 0.001 PHE A 71 TYR 0.038 0.002 TYR A 38 ARG 0.000 0.000 ARG A 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1894.64 seconds wall clock time: 33 minutes 17.16 seconds (1997.16 seconds total)