Starting phenix.real_space_refine on Wed Mar 5 19:54:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gof_34177/03_2025/8gof_34177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gof_34177/03_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_34177/03_2025/8gof_34177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gof_34177/03_2025/8gof_34177.map" model { file = "/net/cci-nas-00/data/ceres_data/8gof_34177/03_2025/8gof_34177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gof_34177/03_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-5624/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: 4.14, per 1000 atoms: 1.25 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: 0.82 Conformation dependent library (CDL) restraints added in 396.3 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: 0.32 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: 0.91 Time building geometry restraints manager: 0.98 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: 5.340 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.460 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:16.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.390 ------------------------------------------------------------------------------- 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 : 0.326 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: 1.4924 time to fit residues: 62.9042 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 : 0.362 ------------------------------------------------------------------------------- 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: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3112 r_free = 0.3112 target = 0.099734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.083884 restraints weight = 4169.229| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.62 r_work: 0.2769 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1945 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= 0.272 Angle : 0.563 5.968 4622 Z= 0.301 Chirality : 0.039 0.121 534 Planarity : 0.005 0.041 559 Dihedral : 7.536 82.019 469 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.85 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 : -1.37 (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 : 0.357 Fit side-chains REVERT: A 88 ASP cc_start: 0.8175 (m-30) cc_final: 0.7944 (m-30) REVERT: A 127 SER cc_start: 0.8852 (m) cc_final: 0.8578 (p) REVERT: A 204 LYS cc_start: 0.7894 (tttm) cc_final: 0.7478 (tttm) REVERT: A 251 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7329 (mm) outliers start: 5 outliers final: 0 residues processed: 42 average time/residue: 1.2318 time to fit residues: 53.4843 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 : 0.375 ------------------------------------------------------------------------------- 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: 0.9980 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 11 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 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.100045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.084333 restraints weight = 4108.163| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.57 r_work: 0.2772 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3391 Z= 0.256 Angle : 0.510 5.397 4622 Z= 0.269 Chirality : 0.039 0.129 534 Planarity : 0.004 0.034 559 Dihedral : 7.321 81.770 469 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.42 % Allowed : 13.11 % 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: -0.47 (0.39), residues: 403 helix: 0.01 (0.27), residues: 320 sheet: None (None), residues: 0 loop : -1.06 (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 0.011 0.001 PHE A 372 TYR 0.013 0.001 TYR A 35 ARG 0.003 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: 5 poor density : 34 time to evaluate : 0.314 Fit side-chains REVERT: A 127 SER cc_start: 0.8849 (m) cc_final: 0.8593 (p) REVERT: A 204 LYS cc_start: 0.7822 (tttm) cc_final: 0.7487 (tttm) REVERT: A 251 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7201 (mm) REVERT: A 293 ASN cc_start: 0.8685 (t0) cc_final: 0.8309 (t0) REVERT: A 393 LYS cc_start: 0.8757 (tppt) cc_final: 0.8530 (tppp) outliers start: 5 outliers final: 0 residues processed: 38 average time/residue: 1.3271 time to fit residues: 52.0383 Evaluate side-chains 35 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 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 = 0.3124 r_free = 0.3124 target = 0.100851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.085094 restraints weight = 4144.255| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.58 r_work: 0.2784 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3391 Z= 0.228 Angle : 0.485 5.377 4622 Z= 0.255 Chirality : 0.038 0.129 534 Planarity : 0.003 0.031 559 Dihedral : 7.144 84.545 469 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.90 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: 0.59 (0.41), residues: 403 helix: 0.80 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.94 (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 0.012 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: 9 poor density : 32 time to evaluate : 0.354 Fit side-chains REVERT: A 162 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7506 (tt) REVERT: A 204 LYS cc_start: 0.7890 (tttm) cc_final: 0.7451 (tttm) REVERT: A 251 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7171 (mm) outliers start: 9 outliers final: 2 residues processed: 38 average time/residue: 1.2386 time to fit residues: 48.6870 Evaluate side-chains 36 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 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 = 0.3151 r_free = 0.3151 target = 0.102822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.086815 restraints weight = 4103.772| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.64 r_work: 0.2817 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2312 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= 0.215 Angle : 0.479 5.350 4622 Z= 0.251 Chirality : 0.038 0.127 534 Planarity : 0.003 0.029 559 Dihedral : 7.076 86.871 469 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.56 % Allowed : 13.39 % Favored : 84.05 % 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: 0.99 (0.42), residues: 403 helix: 1.10 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.86 (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 39 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.343 Fit side-chains REVERT: A 162 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7535 (tt) REVERT: A 204 LYS cc_start: 0.7931 (tttm) cc_final: 0.7504 (tttm) REVERT: A 251 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7185 (mm) outliers start: 9 outliers final: 2 residues processed: 37 average time/residue: 1.3818 time to fit residues: 52.7595 Evaluate side-chains 34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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: 0.6980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3141 r_free = 0.3141 target = 0.102168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.086071 restraints weight = 4226.849| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.67 r_work: 0.2801 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3391 Z= 0.240 Angle : 0.486 5.365 4622 Z= 0.254 Chirality : 0.039 0.129 534 Planarity : 0.003 0.030 559 Dihedral : 7.037 89.253 469 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.28 % Allowed : 13.68 % Favored : 84.05 % 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: 1.19 (0.42), residues: 403 helix: 1.25 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.84 (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 0.012 0.001 TYR A 35 ARG 0.002 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 37 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.319 Fit side-chains REVERT: A 162 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7419 (tt) REVERT: A 204 LYS cc_start: 0.7856 (tttm) cc_final: 0.7416 (tttm) REVERT: A 251 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7117 (mm) outliers start: 8 outliers final: 3 residues processed: 36 average time/residue: 1.3662 time to fit residues: 50.7258 Evaluate side-chains 33 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 251 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: 0.6980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.103288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.087380 restraints weight = 4054.986| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.64 r_work: 0.2823 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2434 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= 0.201 Angle : 0.468 5.331 4622 Z= 0.245 Chirality : 0.038 0.125 534 Planarity : 0.003 0.029 559 Dihedral : 6.789 85.975 469 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.99 % Allowed : 14.53 % Favored : 83.48 % 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: 1.38 (0.42), residues: 403 helix: 1.39 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.85 (0.62), 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 0.011 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 39 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.333 Fit side-chains REVERT: A 162 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7473 (tt) outliers start: 7 outliers final: 3 residues processed: 38 average time/residue: 1.3784 time to fit residues: 53.9502 Evaluate side-chains 34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- 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 = 0.3160 r_free = 0.3160 target = 0.103529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.087690 restraints weight = 4070.444| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.62 r_work: 0.2833 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3391 Z= 0.189 Angle : 0.465 5.326 4622 Z= 0.243 Chirality : 0.038 0.124 534 Planarity : 0.003 0.028 559 Dihedral : 6.900 87.670 469 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.75 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: 1.61 (0.42), residues: 403 helix: 1.56 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.81 (0.62), 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 0.008 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 36 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.323 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 36 average time/residue: 1.3162 time to fit residues: 48.9534 Evaluate side-chains 29 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3138 r_free = 0.3138 target = 0.101851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.085910 restraints weight = 4157.610| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.66 r_work: 0.2797 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3391 Z= 0.253 Angle : 0.496 5.373 4622 Z= 0.258 Chirality : 0.040 0.131 534 Planarity : 0.003 0.029 559 Dihedral : 7.070 89.004 469 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.85 % Allowed : 16.52 % 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: 1.59 (0.42), residues: 403 helix: 1.55 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.79 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.003 0.000 HIS A 114 PHE 0.011 0.001 PHE A 372 TYR 0.012 0.001 TYR A 35 ARG 0.008 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 : 0.379 Fit side-chains REVERT: A 204 LYS cc_start: 0.7990 (tttm) cc_final: 0.7550 (tttm) REVERT: A 319 ILE cc_start: 0.7738 (mt) cc_final: 0.7455 (mp) outliers start: 3 outliers final: 1 residues processed: 33 average time/residue: 1.5082 time to fit residues: 51.2863 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 : 0.339 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 25 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 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.103322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.087379 restraints weight = 4046.590| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.64 r_work: 0.2823 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3391 Z= 0.205 Angle : 0.474 5.342 4622 Z= 0.247 Chirality : 0.038 0.126 534 Planarity : 0.003 0.029 559 Dihedral : 6.990 89.346 469 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.85 % Allowed : 16.52 % 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: 1.75 (0.42), residues: 403 helix: 1.66 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.77 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.003 0.000 HIS A 114 PHE 0.011 0.001 PHE A 372 TYR 0.010 0.001 TYR A 92 ARG 0.007 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 34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.366 Fit side-chains REVERT: A 204 LYS cc_start: 0.8015 (tttm) cc_final: 0.7582 (tttm) REVERT: A 319 ILE cc_start: 0.7732 (mt) cc_final: 0.7450 (mp) outliers start: 3 outliers final: 1 residues processed: 33 average time/residue: 1.5611 time to fit residues: 53.0248 Evaluate side-chains 31 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 39 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.113300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.097914 restraints weight = 3925.512| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.53 r_work: 0.2838 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2548 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= 0.200 Angle : 0.472 5.333 4622 Z= 0.247 Chirality : 0.038 0.125 534 Planarity : 0.003 0.029 559 Dihedral : 6.862 86.970 469 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.28 % Allowed : 17.09 % 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: 1.84 (0.42), residues: 403 helix: 1.72 (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 0.010 0.001 TYR A 92 ARG 0.008 0.000 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2424.53 seconds wall clock time: 42 minutes 13.02 seconds (2533.02 seconds total)