Starting phenix.real_space_refine on Thu Jul 18 19:05:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcs_18334/07_2024/8qcs_18334.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcs_18334/07_2024/8qcs_18334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcs_18334/07_2024/8qcs_18334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcs_18334/07_2024/8qcs_18334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcs_18334/07_2024/8qcs_18334.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcs_18334/07_2024/8qcs_18334.cif" } resolution = 2.9 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= 0.003 sd= 0.097 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 18 5.16 5 C 2156 2.51 5 N 500 2.21 5 O 567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 136": "OE1" <-> "OE2" Residue "A ASP 266": "OD1" <-> "OD2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 457": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3241 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3241 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 17, 'TRANS': 399} Time building chain proxies: 2.52, per 1000 atoms: 0.78 Number of scatterers: 3241 At special positions: 0 Unit cell: (80.22, 55.008, 65.322, 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 18 16.00 O 567 8.00 N 500 7.00 C 2156 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: 1.81 Conformation dependent library (CDL) restraints added in 596.0 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 90.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 105 through 127 removed outlier: 4.213A pdb=" N VAL A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 removed outlier: 4.068A pdb=" N GLY A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.719A pdb=" N ILE A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.722A pdb=" N LEU A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.712A pdb=" N THR A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 193 " --> pdb=" O TRP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 219 removed outlier: 3.555A pdb=" N THR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.349A pdb=" N ARG A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.502A pdb=" N THR A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 266 through 296 Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.777A pdb=" N ASP A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 319 removed outlier: 6.226A pdb=" N GLU A 317 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU A 318 " --> pdb=" O PRO A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 329 removed outlier: 3.542A pdb=" N PHE A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 363 removed outlier: 3.709A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 393 removed outlier: 4.112A pdb=" N GLY A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 418 removed outlier: 3.518A pdb=" N MET A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 424 through 440 removed outlier: 3.721A pdb=" N VAL A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 453 Processing helix chain 'A' and resid 458 through 489 removed outlier: 3.768A pdb=" N SER A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.556A pdb=" N LEU A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) 255 hydrogen bonds defined for protein. 756 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: 0.96 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 961 1.34 - 1.46: 641 1.46 - 1.57: 1693 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 3323 Sorted by residual: bond pdb=" N ILE A 427 " pdb=" CA ILE A 427 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.52e+00 bond pdb=" N GLN A 308 " pdb=" CA GLN A 308 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.30e-02 5.92e+03 5.28e+00 bond pdb=" N ASP A 169 " pdb=" CA ASP A 169 " ideal model delta sigma weight residual 1.457 1.486 -0.030 1.33e-02 5.65e+03 4.95e+00 bond pdb=" CB GLN A 306 " pdb=" CG GLN A 306 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" C ILE A 427 " pdb=" N VAL A 428 " ideal model delta sigma weight residual 1.335 1.324 0.011 1.20e-02 6.94e+03 8.92e-01 ... (remaining 3318 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.91: 88 106.91 - 113.68: 1859 113.68 - 120.45: 1353 120.45 - 127.22: 1200 127.22 - 133.99: 34 Bond angle restraints: 4534 Sorted by residual: angle pdb=" C ALA A 307 " pdb=" N GLN A 308 " pdb=" CA GLN A 308 " ideal model delta sigma weight residual 120.68 115.80 4.88 1.70e+00 3.46e-01 8.23e+00 angle pdb=" N GLN A 308 " pdb=" CA GLN A 308 " pdb=" C GLN A 308 " ideal model delta sigma weight residual 112.23 108.88 3.35 1.26e+00 6.30e-01 7.09e+00 angle pdb=" N LEU A 220 " pdb=" CA LEU A 220 " pdb=" C LEU A 220 " ideal model delta sigma weight residual 109.81 115.56 -5.75 2.21e+00 2.05e-01 6.76e+00 angle pdb=" N LYS A 396 " pdb=" CA LYS A 396 " pdb=" C LYS A 396 " ideal model delta sigma weight residual 108.34 111.55 -3.21 1.31e+00 5.83e-01 6.02e+00 angle pdb=" CA LEU A 269 " pdb=" CB LEU A 269 " pdb=" CG LEU A 269 " ideal model delta sigma weight residual 116.30 124.77 -8.47 3.50e+00 8.16e-02 5.85e+00 ... (remaining 4529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 1697 17.51 - 35.02: 168 35.02 - 52.53: 34 52.53 - 70.05: 13 70.05 - 87.56: 2 Dihedral angle restraints: 1914 sinusoidal: 714 harmonic: 1200 Sorted by residual: dihedral pdb=" CA ASP A 421 " pdb=" CB ASP A 421 " pdb=" CG ASP A 421 " pdb=" OD1 ASP A 421 " ideal model delta sinusoidal sigma weight residual -30.00 -86.73 56.73 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA TYR A 117 " pdb=" C TYR A 117 " pdb=" N SER A 118 " pdb=" CA SER A 118 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA THR A 440 " pdb=" C THR A 440 " pdb=" N GLY A 441 " pdb=" CA GLY A 441 " ideal model delta harmonic sigma weight residual 180.00 164.17 15.83 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 1911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 316 0.026 - 0.051: 130 0.051 - 0.077: 66 0.077 - 0.102: 23 0.102 - 0.128: 8 Chirality restraints: 543 Sorted by residual: chirality pdb=" CA ILE A 427 " pdb=" N ILE A 427 " pdb=" C ILE A 427 " pdb=" CB ILE A 427 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.15e-01 chirality pdb=" CA TYR A 117 " pdb=" N TYR A 117 " pdb=" C TYR A 117 " pdb=" CB TYR A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.02e-01 ... (remaining 540 not shown) Planarity restraints: 550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 443 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 444 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 444 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 444 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 255 " -0.020 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO A 256 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 256 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 256 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 256 " 0.018 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO A 257 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " 0.015 5.00e-02 4.00e+02 ... (remaining 547 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1003 2.82 - 3.34: 3277 3.34 - 3.86: 5409 3.86 - 4.38: 6478 4.38 - 4.90: 10937 Nonbonded interactions: 27104 Sorted by model distance: nonbonded pdb=" ND2 ASN A 262 " pdb=" OE1 GLU A 367 " model vdw 2.301 2.520 nonbonded pdb=" O ILE A 415 " pdb=" OG1 THR A 419 " model vdw 2.380 2.440 nonbonded pdb=" OH TYR A 319 " pdb=" OG SER A 458 " model vdw 2.383 2.440 nonbonded pdb=" O GLY A 504 " pdb=" OG1 THR A 508 " model vdw 2.419 2.440 nonbonded pdb=" NE1 TRP A 189 " pdb=" OG1 THR A 286 " model vdw 2.424 2.520 ... (remaining 27099 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.700 Find NCS groups from input model: 0.240 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:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3323 Z= 0.191 Angle : 0.571 8.467 4534 Z= 0.294 Chirality : 0.038 0.128 543 Planarity : 0.003 0.034 550 Dihedral : 15.225 87.558 1150 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 20.11 % Favored : 79.89 % 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: 0.62 (0.39), residues: 415 helix: 0.91 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -1.18 (0.58), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.008 0.001 PHE A 162 TYR 0.016 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.371 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 1.2549 time to fit residues: 51.6973 Evaluate side-chains 37 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 184 ASN A 369 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3323 Z= 0.181 Angle : 0.599 7.561 4534 Z= 0.306 Chirality : 0.039 0.146 543 Planarity : 0.004 0.030 550 Dihedral : 4.085 16.306 446 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.98 % Allowed : 18.13 % Favored : 79.89 % 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 (0.41), residues: 415 helix: 1.74 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.68 (0.57), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 500 HIS 0.001 0.000 HIS A 198 PHE 0.011 0.001 PHE A 496 TYR 0.023 0.001 TYR A 117 ARG 0.002 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.399 Fit side-chains REVERT: A 136 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6633 (mt-10) REVERT: A 277 MET cc_start: 0.8234 (ttp) cc_final: 0.8021 (ttm) REVERT: A 390 LEU cc_start: 0.7397 (mt) cc_final: 0.6614 (tt) REVERT: A 409 SER cc_start: 0.9145 (t) cc_final: 0.8909 (m) outliers start: 7 outliers final: 0 residues processed: 55 average time/residue: 1.0205 time to fit residues: 58.0863 Evaluate side-chains 40 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.0060 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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: 0.7803 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3323 Z= 0.187 Angle : 0.572 7.908 4534 Z= 0.289 Chirality : 0.039 0.145 543 Planarity : 0.004 0.029 550 Dihedral : 4.015 15.374 446 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.83 % Allowed : 19.55 % Favored : 77.62 % 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: 1.83 (0.41), residues: 415 helix: 1.97 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.74 (0.57), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 500 HIS 0.001 0.001 HIS A 198 PHE 0.011 0.001 PHE A 496 TYR 0.025 0.001 TYR A 117 ARG 0.001 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.360 Fit side-chains REVERT: A 136 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6638 (mt-10) REVERT: A 277 MET cc_start: 0.8194 (ttp) cc_final: 0.7968 (ttm) REVERT: A 390 LEU cc_start: 0.7515 (mt) cc_final: 0.6752 (tt) REVERT: A 409 SER cc_start: 0.9156 (t) cc_final: 0.8923 (m) outliers start: 10 outliers final: 2 residues processed: 48 average time/residue: 1.0159 time to fit residues: 50.4926 Evaluate side-chains 41 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.0000 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3323 Z= 0.182 Angle : 0.568 8.570 4534 Z= 0.284 Chirality : 0.039 0.152 543 Planarity : 0.003 0.029 550 Dihedral : 4.023 16.238 446 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.12 % Allowed : 19.55 % Favored : 77.34 % 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: 1.94 (0.42), residues: 415 helix: 2.06 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.81 (0.56), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 500 HIS 0.001 0.001 HIS A 198 PHE 0.010 0.001 PHE A 496 TYR 0.025 0.001 TYR A 117 ARG 0.001 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.363 Fit side-chains REVERT: A 126 ILE cc_start: 0.9130 (tp) cc_final: 0.8797 (tp) REVERT: A 136 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6652 (mt-10) REVERT: A 277 MET cc_start: 0.8122 (ttp) cc_final: 0.7919 (ttm) REVERT: A 388 CYS cc_start: 0.6669 (OUTLIER) cc_final: 0.5465 (m) REVERT: A 390 LEU cc_start: 0.7372 (mt) cc_final: 0.6563 (tt) REVERT: A 409 SER cc_start: 0.9068 (t) cc_final: 0.8827 (m) outliers start: 11 outliers final: 1 residues processed: 48 average time/residue: 0.9959 time to fit residues: 49.5995 Evaluate side-chains 41 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3323 Z= 0.200 Angle : 0.570 7.658 4534 Z= 0.284 Chirality : 0.039 0.155 543 Planarity : 0.004 0.029 550 Dihedral : 4.023 16.086 446 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.68 % Allowed : 18.98 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.42), residues: 415 helix: 2.14 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.83 (0.56), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.010 0.001 PHE A 496 TYR 0.025 0.001 TYR A 117 ARG 0.001 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 0.375 Fit side-chains REVERT: A 126 ILE cc_start: 0.9130 (tp) cc_final: 0.8797 (tp) REVERT: A 136 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6627 (mt-10) REVERT: A 277 MET cc_start: 0.8097 (ttp) cc_final: 0.7874 (ttm) REVERT: A 388 CYS cc_start: 0.6602 (OUTLIER) cc_final: 0.5465 (m) REVERT: A 390 LEU cc_start: 0.7413 (mt) cc_final: 0.6657 (tt) REVERT: A 409 SER cc_start: 0.9079 (t) cc_final: 0.8827 (m) outliers start: 13 outliers final: 2 residues processed: 46 average time/residue: 1.0216 time to fit residues: 48.7530 Evaluate side-chains 41 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 13 optimal weight: 0.0030 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3323 Z= 0.170 Angle : 0.560 7.922 4534 Z= 0.279 Chirality : 0.039 0.152 543 Planarity : 0.003 0.029 550 Dihedral : 3.992 16.672 446 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.83 % Allowed : 20.96 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.42), residues: 415 helix: 2.18 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.80 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 500 HIS 0.001 0.000 HIS A 198 PHE 0.010 0.001 PHE A 496 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.362 Fit side-chains REVERT: A 126 ILE cc_start: 0.9088 (tp) cc_final: 0.8778 (tp) REVERT: A 136 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6642 (mt-10) REVERT: A 277 MET cc_start: 0.8080 (ttp) cc_final: 0.7878 (ttm) REVERT: A 388 CYS cc_start: 0.6536 (OUTLIER) cc_final: 0.5493 (m) REVERT: A 390 LEU cc_start: 0.7410 (mt) cc_final: 0.6692 (tt) REVERT: A 409 SER cc_start: 0.9043 (t) cc_final: 0.8810 (m) outliers start: 10 outliers final: 2 residues processed: 52 average time/residue: 0.9844 time to fit residues: 53.0412 Evaluate side-chains 43 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3323 Z= 0.173 Angle : 0.557 8.162 4534 Z= 0.278 Chirality : 0.039 0.152 543 Planarity : 0.003 0.029 550 Dihedral : 3.997 16.735 446 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.70 % Allowed : 22.66 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.41), residues: 415 helix: 2.15 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.70 (0.56), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.010 0.001 PHE A 496 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.364 Fit side-chains REVERT: A 126 ILE cc_start: 0.9078 (tp) cc_final: 0.8776 (tp) REVERT: A 136 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6643 (mt-10) REVERT: A 154 MET cc_start: 0.9193 (mtm) cc_final: 0.8927 (mtm) REVERT: A 388 CYS cc_start: 0.6388 (OUTLIER) cc_final: 0.5783 (m) REVERT: A 390 LEU cc_start: 0.7321 (mt) cc_final: 0.6572 (tt) REVERT: A 409 SER cc_start: 0.9059 (t) cc_final: 0.8853 (m) outliers start: 6 outliers final: 2 residues processed: 47 average time/residue: 1.0312 time to fit residues: 50.2927 Evaluate side-chains 43 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3323 Z= 0.189 Angle : 0.557 7.574 4534 Z= 0.279 Chirality : 0.039 0.154 543 Planarity : 0.003 0.030 550 Dihedral : 4.004 16.978 446 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.55 % Allowed : 22.66 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.41), residues: 415 helix: 2.18 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.69 (0.56), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 500 HIS 0.001 0.001 HIS A 198 PHE 0.009 0.001 PHE A 496 TYR 0.025 0.001 TYR A 117 ARG 0.001 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.354 Fit side-chains REVERT: A 126 ILE cc_start: 0.9086 (tp) cc_final: 0.8774 (tp) REVERT: A 136 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6648 (mt-10) REVERT: A 388 CYS cc_start: 0.6237 (OUTLIER) cc_final: 0.5586 (m) REVERT: A 409 SER cc_start: 0.9067 (t) cc_final: 0.8802 (m) outliers start: 9 outliers final: 2 residues processed: 46 average time/residue: 1.1553 time to fit residues: 54.9486 Evaluate side-chains 43 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3323 Z= 0.195 Angle : 0.575 8.857 4534 Z= 0.285 Chirality : 0.039 0.155 543 Planarity : 0.004 0.030 550 Dihedral : 4.031 16.995 446 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.70 % Allowed : 24.08 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.41), residues: 415 helix: 2.17 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.66 (0.56), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.009 0.001 PHE A 334 TYR 0.025 0.001 TYR A 117 ARG 0.001 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.354 Fit side-chains REVERT: A 126 ILE cc_start: 0.9094 (tp) cc_final: 0.8786 (tp) REVERT: A 136 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6660 (mt-10) REVERT: A 154 MET cc_start: 0.9192 (mtm) cc_final: 0.8953 (mtm) REVERT: A 388 CYS cc_start: 0.6367 (OUTLIER) cc_final: 0.5731 (m) REVERT: A 409 SER cc_start: 0.9065 (t) cc_final: 0.8819 (m) outliers start: 6 outliers final: 2 residues processed: 45 average time/residue: 1.1389 time to fit residues: 53.0604 Evaluate side-chains 42 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.0070 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3323 Z= 0.173 Angle : 0.564 8.792 4534 Z= 0.280 Chirality : 0.039 0.154 543 Planarity : 0.003 0.029 550 Dihedral : 3.990 16.360 446 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.13 % Allowed : 24.65 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.41), residues: 415 helix: 2.22 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.68 (0.57), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 500 HIS 0.001 0.000 HIS A 198 PHE 0.009 0.001 PHE A 496 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.353 Fit side-chains REVERT: A 126 ILE cc_start: 0.9073 (tp) cc_final: 0.8774 (tp) REVERT: A 136 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6652 (mt-10) REVERT: A 154 MET cc_start: 0.9180 (mtm) cc_final: 0.8941 (mtm) REVERT: A 279 TYR cc_start: 0.7035 (t80) cc_final: 0.5855 (m-80) REVERT: A 388 CYS cc_start: 0.6417 (OUTLIER) cc_final: 0.5909 (m) REVERT: A 409 SER cc_start: 0.9019 (t) cc_final: 0.8767 (m) outliers start: 4 outliers final: 2 residues processed: 43 average time/residue: 1.2271 time to fit residues: 54.6807 Evaluate side-chains 43 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106451 restraints weight = 4172.091| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.14 r_work: 0.3044 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3323 Z= 0.189 Angle : 0.569 8.686 4534 Z= 0.282 Chirality : 0.039 0.155 543 Planarity : 0.003 0.030 550 Dihedral : 4.014 16.349 446 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.70 % Allowed : 23.80 % Favored : 74.50 % 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: 2.24 (0.42), residues: 415 helix: 2.24 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.68 (0.56), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.009 0.001 PHE A 496 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1500.73 seconds wall clock time: 28 minutes 44.17 seconds (1724.17 seconds total)