Starting phenix.real_space_refine on Tue Feb 11 00:50:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gof_34177/02_2025/8gof_34177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gof_34177/02_2025/8gof_34177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gof_34177/02_2025/8gof_34177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gof_34177/02_2025/8gof_34177.map" model { file = "/net/cci-nas-00/data/ceres_data/8gof_34177/02_2025/8gof_34177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gof_34177/02_2025/8gof_34177.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 10 5.16 5 C 2192 2.51 5 N 545 2.21 5 O 552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3299 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3268 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 14, 'TRANS': 392} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'LYA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.42, per 1000 atoms: 1.04 Number of scatterers: 3299 At special positions: 0 Unit cell: (80, 72, 66, 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 10 16.00 O 552 8.00 N 545 7.00 C 2192 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: 1.19 Conformation dependent library (CDL) restraints added in 557.6 milliseconds 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 83.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 25 through 39 removed outlier: 3.520A pdb=" N CYS A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR A 31 " --> pdb=" O HIS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 60 through 68 removed outlier: 3.517A pdb=" N ASN A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 removed outlier: 3.716A pdb=" N TYR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 removed outlier: 4.241A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 113 removed outlier: 3.524A pdb=" N PHE A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.517A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 removed outlier: 4.402A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 176 removed outlier: 3.667A pdb=" N VAL A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 202 removed outlier: 3.827A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.886A pdb=" N ASP A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 278 through 296 removed outlier: 3.558A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 305 through 324 removed outlier: 3.698A pdb=" N THR A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 329 through 333 removed outlier: 3.889A pdb=" N ALA A 332 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG A 333 " --> pdb=" O ARG A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 333' Processing helix chain 'A' and resid 335 through 355 removed outlier: 3.549A pdb=" N THR A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 388 removed outlier: 3.534A pdb=" N PHE A 369 " --> pdb=" O CYS A 365 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 392 through 418 removed outlier: 3.520A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 453 removed outlier: 3.504A pdb=" N GLN A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 654 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: 0.90 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 987 1.34 - 1.46: 765 1.46 - 1.57: 1623 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3391 Sorted by residual: bond pdb=" N MET A 130 " pdb=" CA MET A 130 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.04e+00 bond pdb=" C12 LYA A 601 " pdb=" N11 LYA A 601 " ideal model delta sigma weight residual 1.340 1.370 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C10 LYA A 601 " pdb=" N11 LYA A 601 " ideal model delta sigma weight residual 1.384 1.355 0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C VAL A 81 " pdb=" O VAL A 81 " ideal model delta sigma weight residual 1.240 1.223 0.017 1.26e-02 6.30e+03 1.82e+00 bond pdb=" C17 LYA A 601 " pdb=" N16 LYA A 601 " ideal model delta sigma weight residual 1.305 1.331 -0.026 2.00e-02 2.50e+03 1.72e+00 ... (remaining 3386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 4424 1.62 - 3.24: 153 3.24 - 4.86: 32 4.86 - 6.48: 8 6.48 - 8.10: 5 Bond angle restraints: 4622 Sorted by residual: angle pdb=" N PHE A 103 " pdb=" CA PHE A 103 " pdb=" C PHE A 103 " ideal model delta sigma weight residual 111.40 105.48 5.92 1.22e+00 6.72e-01 2.35e+01 angle pdb=" C TYR A 92 " pdb=" CA TYR A 92 " pdb=" CB TYR A 92 " ideal model delta sigma weight residual 110.42 102.32 8.10 1.99e+00 2.53e-01 1.66e+01 angle pdb=" N LEU A 162 " pdb=" CA LEU A 162 " pdb=" C LEU A 162 " ideal model delta sigma weight residual 112.23 107.69 4.54 1.26e+00 6.30e-01 1.30e+01 angle pdb=" N ILE A 329 " pdb=" CA ILE A 329 " pdb=" C ILE A 329 " ideal model delta sigma weight residual 112.96 109.62 3.34 1.00e+00 1.00e+00 1.12e+01 angle pdb=" N VAL A 428 " pdb=" CA VAL A 428 " pdb=" C VAL A 428 " ideal model delta sigma weight residual 111.17 115.69 -4.52 1.38e+00 5.25e-01 1.07e+01 ... (remaining 4617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 1772 16.07 - 32.13: 132 32.13 - 48.19: 31 48.19 - 64.26: 11 64.26 - 80.32: 2 Dihedral angle restraints: 1948 sinusoidal: 750 harmonic: 1198 Sorted by residual: dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 154.19 25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CB ARG A 373 " pdb=" CG ARG A 373 " pdb=" CD ARG A 373 " pdb=" NE ARG A 373 " ideal model delta sinusoidal sigma weight residual 60.00 118.74 -58.74 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA VAL A 418 " pdb=" C VAL A 418 " pdb=" N SER A 419 " pdb=" CA SER A 419 " ideal model delta harmonic sigma weight residual 180.00 -164.62 -15.38 0 5.00e+00 4.00e-02 9.46e+00 ... (remaining 1945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 343 0.041 - 0.081: 157 0.081 - 0.122: 26 0.122 - 0.163: 7 0.163 - 0.203: 1 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ARG A 42 " pdb=" N ARG A 42 " pdb=" C ARG A 42 " pdb=" CB ARG A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL A 288 " pdb=" CA VAL A 288 " pdb=" CG1 VAL A 288 " pdb=" CG2 VAL A 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA LYS A 57 " pdb=" N LYS A 57 " pdb=" C LYS A 57 " pdb=" CB LYS A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 531 not shown) Planarity restraints: 559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 LYA A 601 " -0.041 2.00e-02 2.50e+03 1.04e-01 1.36e+02 pdb=" C23 LYA A 601 " 0.127 2.00e-02 2.50e+03 pdb=" C4 LYA A 601 " 0.097 2.00e-02 2.50e+03 pdb=" N22 LYA A 601 " -0.163 2.00e-02 2.50e+03 pdb=" O21 LYA A 601 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.044 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO A 70 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 41 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C ILE A 41 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE A 41 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 42 " 0.013 2.00e-02 2.50e+03 ... (remaining 556 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 986 2.79 - 3.32: 2929 3.32 - 3.85: 5651 3.85 - 4.37: 7087 4.37 - 4.90: 11655 Nonbonded interactions: 28308 Sorted by model distance: nonbonded pdb=" O VAL A 83 " pdb=" OG1 THR A 87 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASP A 88 " pdb=" OH TYR A 92 " model vdw 2.271 3.040 nonbonded pdb=" O VAL A 304 " pdb=" OH TYR A 366 " model vdw 2.278 3.040 nonbonded pdb=" O LEU A 32 " pdb=" OH TYR A 136 " model vdw 2.298 3.040 nonbonded pdb=" O VAL A 380 " pdb=" OG1 THR A 384 " model vdw 2.324 3.040 ... (remaining 28303 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: 1.820 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.650 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.006 0.056 3391 Z= 0.412 Angle : 0.799 8.103 4622 Z= 0.453 Chirality : 0.046 0.203 534 Planarity : 0.007 0.104 559 Dihedral : 13.255 80.321 1178 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % 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: -6.52 (0.22), residues: 403 helix: -4.45 (0.11), residues: 322 sheet: None (None), residues: 0 loop : -2.16 (0.54), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 107 HIS 0.002 0.001 HIS A 114 PHE 0.016 0.002 PHE A 37 TYR 0.011 0.002 TYR A 92 ARG 0.003 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.385 Fit side-chains REVERT: A 60 THR cc_start: 0.8565 (m) cc_final: 0.8328 (p) REVERT: A 277 ASN cc_start: 0.8309 (t0) cc_final: 0.7975 (t160) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 1.5450 time to fit residues: 65.1785 Evaluate side-chains 29 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 293 ASN A 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.099651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.083802 restraints weight = 4176.212| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.62 r_work: 0.2768 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3391 Z= 0.273 Angle : 0.564 5.951 4622 Z= 0.301 Chirality : 0.039 0.131 534 Planarity : 0.005 0.041 559 Dihedral : 7.547 82.649 469 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.42 % Allowed : 11.11 % Favored : 87.46 % 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: -2.73 (0.34), residues: 403 helix: -1.69 (0.23), residues: 320 sheet: None (None), residues: 0 loop : -1.36 (0.61), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.012 0.001 PHE A 372 TYR 0.014 0.001 TYR A 35 ARG 0.005 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.367 Fit side-chains REVERT: A 88 ASP cc_start: 0.8174 (m-30) cc_final: 0.7943 (m-30) REVERT: A 127 SER cc_start: 0.8857 (m) cc_final: 0.8581 (p) REVERT: A 204 LYS cc_start: 0.7888 (tttm) cc_final: 0.7474 (tttm) REVERT: A 251 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7387 (mm) outliers start: 5 outliers final: 0 residues processed: 42 average time/residue: 1.2104 time to fit residues: 52.5272 Evaluate side-chains 37 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 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 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.101178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.085529 restraints weight = 4089.881| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.57 r_work: 0.2793 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3391 Z= 0.210 Angle : 0.489 5.381 4622 Z= 0.259 Chirality : 0.038 0.125 534 Planarity : 0.004 0.032 559 Dihedral : 7.269 85.503 469 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.71 % Allowed : 12.82 % Favored : 85.47 % 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: -0.41 (0.39), residues: 403 helix: 0.05 (0.27), residues: 320 sheet: None (None), residues: 0 loop : -1.04 (0.61), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.012 0.001 PHE A 372 TYR 0.012 0.001 TYR A 35 ARG 0.004 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.356 Fit side-chains REVERT: A 127 SER cc_start: 0.8822 (m) cc_final: 0.8556 (p) REVERT: A 204 LYS cc_start: 0.7831 (tttm) cc_final: 0.7415 (tttm) REVERT: A 251 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7180 (mm) REVERT: A 393 LYS cc_start: 0.8751 (tppt) cc_final: 0.8533 (tppp) outliers start: 6 outliers final: 0 residues processed: 38 average time/residue: 1.3100 time to fit residues: 51.3930 Evaluate side-chains 34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.099780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.083925 restraints weight = 4169.586| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.58 r_work: 0.2767 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3391 Z= 0.276 Angle : 0.508 5.389 4622 Z= 0.266 Chirality : 0.040 0.134 534 Planarity : 0.004 0.032 559 Dihedral : 7.196 86.011 469 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.28 % Allowed : 13.11 % Favored : 84.62 % 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: 0.46 (0.41), residues: 403 helix: 0.71 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.95 (0.61), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.010 0.001 PHE A 372 TYR 0.014 0.001 TYR A 35 ARG 0.003 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.324 Fit side-chains REVERT: A 162 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7506 (tt) REVERT: A 204 LYS cc_start: 0.7847 (tttm) cc_final: 0.7398 (tttm) REVERT: A 251 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7178 (mm) outliers start: 8 outliers final: 2 residues processed: 38 average time/residue: 1.3660 time to fit residues: 53.6100 Evaluate side-chains 37 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 277 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.102635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.086669 restraints weight = 4117.157| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.65 r_work: 0.2812 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3391 Z= 0.216 Angle : 0.480 5.330 4622 Z= 0.252 Chirality : 0.038 0.128 534 Planarity : 0.003 0.030 559 Dihedral : 7.096 88.412 469 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.56 % Allowed : 12.82 % Favored : 84.62 % 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: 0.96 (0.41), residues: 403 helix: 1.07 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.85 (0.61), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 PHE 0.011 0.001 PHE A 372 TYR 0.011 0.001 TYR A 35 ARG 0.003 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.374 Fit side-chains REVERT: A 162 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7472 (tt) REVERT: A 204 LYS cc_start: 0.7902 (tttm) cc_final: 0.7481 (tttm) REVERT: A 251 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7151 (mm) outliers start: 9 outliers final: 2 residues processed: 36 average time/residue: 1.4384 time to fit residues: 53.4202 Evaluate side-chains 33 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 251 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.0070 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3164 r_free = 0.3164 target = 0.103778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.087731 restraints weight = 4190.264| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.67 r_work: 0.2828 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3391 Z= 0.190 Angle : 0.463 5.315 4622 Z= 0.243 Chirality : 0.038 0.125 534 Planarity : 0.003 0.028 559 Dihedral : 6.750 84.624 469 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.56 % Allowed : 13.11 % Favored : 84.33 % 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: 1.32 (0.42), residues: 403 helix: 1.34 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -0.79 (0.61), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 PHE 0.011 0.001 PHE A 372 TYR 0.010 0.001 TYR A 35 ARG 0.003 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.374 Fit side-chains REVERT: A 162 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7532 (tt) REVERT: A 204 LYS cc_start: 0.7984 (tttm) cc_final: 0.7563 (tttm) outliers start: 9 outliers final: 3 residues processed: 40 average time/residue: 1.2589 time to fit residues: 52.0985 Evaluate side-chains 35 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.086859 restraints weight = 4070.816| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.64 r_work: 0.2814 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3391 Z= 0.226 Angle : 0.479 5.348 4622 Z= 0.250 Chirality : 0.039 0.129 534 Planarity : 0.003 0.029 559 Dihedral : 6.995 88.908 469 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.71 % Allowed : 15.38 % Favored : 82.91 % 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: 1.48 (0.42), residues: 403 helix: 1.46 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.76 (0.62), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 PHE 0.010 0.001 PHE A 372 TYR 0.012 0.001 TYR A 35 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.364 Fit side-chains REVERT: A 204 LYS cc_start: 0.8032 (tttm) cc_final: 0.7610 (tttm) REVERT: A 298 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8831 (t) REVERT: A 303 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8065 (ttp80) outliers start: 6 outliers final: 1 residues processed: 37 average time/residue: 1.4529 time to fit residues: 55.2372 Evaluate side-chains 33 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 298 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.086484 restraints weight = 4124.840| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.65 r_work: 0.2810 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3391 Z= 0.225 Angle : 0.478 5.351 4622 Z= 0.249 Chirality : 0.038 0.129 534 Planarity : 0.003 0.029 559 Dihedral : 7.057 86.772 469 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.14 % Allowed : 15.67 % Favored : 83.19 % 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: 1.63 (0.42), residues: 403 helix: 1.56 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.72 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 PHE 0.011 0.001 PHE A 372 TYR 0.012 0.001 TYR A 35 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.351 Fit side-chains REVERT: A 204 LYS cc_start: 0.8065 (tttm) cc_final: 0.7639 (tttm) REVERT: A 298 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8836 (t) REVERT: A 303 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8075 (ttp80) REVERT: A 319 ILE cc_start: 0.7793 (mt) cc_final: 0.7512 (mp) outliers start: 4 outliers final: 1 residues processed: 36 average time/residue: 1.5712 time to fit residues: 58.1304 Evaluate side-chains 33 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 298 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 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 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.101847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.085730 restraints weight = 4146.644| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.66 r_work: 0.2800 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3391 Z= 0.243 Angle : 0.487 5.358 4622 Z= 0.253 Chirality : 0.039 0.130 534 Planarity : 0.003 0.029 559 Dihedral : 7.092 84.295 469 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.85 % Allowed : 16.24 % Favored : 82.91 % 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: 1.67 (0.42), residues: 403 helix: 1.58 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.66 (0.64), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 PHE 0.011 0.001 PHE A 372 TYR 0.012 0.001 TYR A 35 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.331 Fit side-chains REVERT: A 204 LYS cc_start: 0.8002 (tttm) cc_final: 0.7555 (tttm) REVERT: A 303 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8132 (ttp80) REVERT: A 319 ILE cc_start: 0.7716 (mt) cc_final: 0.7427 (mp) outliers start: 3 outliers final: 1 residues processed: 33 average time/residue: 1.5533 time to fit residues: 52.6588 Evaluate side-chains 32 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 0.0570 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.103410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.087478 restraints weight = 4039.832| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.59 r_work: 0.2823 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3391 Z= 0.212 Angle : 0.474 5.331 4622 Z= 0.247 Chirality : 0.038 0.127 534 Planarity : 0.003 0.029 559 Dihedral : 7.046 84.014 469 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.85 % Allowed : 16.24 % Favored : 82.91 % 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: 1.78 (0.42), residues: 403 helix: 1.66 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.62 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 PHE 0.010 0.001 PHE A 372 TYR 0.011 0.001 TYR A 35 ARG 0.002 0.000 ARG A 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.362 Fit side-chains REVERT: A 298 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8809 (t) REVERT: A 303 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7987 (ttp80) REVERT: A 319 ILE cc_start: 0.7678 (mt) cc_final: 0.7394 (mp) outliers start: 3 outliers final: 1 residues processed: 32 average time/residue: 1.5684 time to fit residues: 51.7204 Evaluate side-chains 32 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 298 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.103917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.087956 restraints weight = 4058.914| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.64 r_work: 0.2831 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3391 Z= 0.191 Angle : 0.463 5.328 4622 Z= 0.242 Chirality : 0.038 0.124 534 Planarity : 0.003 0.029 559 Dihedral : 6.976 85.406 469 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.42 % Allowed : 15.95 % Favored : 82.62 % 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: 1.89 (0.42), residues: 403 helix: 1.74 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.62 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 PHE 0.011 0.001 PHE A 372 TYR 0.011 0.001 TYR A 92 ARG 0.002 0.000 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.99 seconds wall clock time: 43 minutes 4.29 seconds (2584.29 seconds total)