Starting phenix.real_space_refine on Mon Feb 10 22:30:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7t_39827/02_2025/8z7t_39827.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7t_39827/02_2025/8z7t_39827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7t_39827/02_2025/8z7t_39827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7t_39827/02_2025/8z7t_39827.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7t_39827/02_2025/8z7t_39827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7t_39827/02_2025/8z7t_39827.cif" } resolution = 3.39 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= 0.002 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2099 2.51 5 N 464 2.21 5 O 532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 3110 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3098 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UEG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.59, per 1000 atoms: 0.83 Number of scatterers: 3110 At special positions: 0 Unit cell: (63, 68, 69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 532 8.00 N 464 7.00 C 2099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 368.0 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.586A pdb=" N ASN A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.727A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 4.373A pdb=" N VAL A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 99 removed outlier: 3.661A pdb=" N ILE A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 131 removed outlier: 4.323A pdb=" N THR A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 164 Processing helix chain 'A' and resid 168 through 189 Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.569A pdb=" N PHE A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 307 removed outlier: 4.232A pdb=" N TRP A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 337 removed outlier: 4.222A pdb=" N TYR A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 319 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 366 Processing helix chain 'A' and resid 368 through 398 Processing helix chain 'A' and resid 402 through 426 removed outlier: 3.528A pdb=" N VAL A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 461 removed outlier: 3.720A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 735 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: 0.84 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 890 1.35 - 1.47: 936 1.47 - 1.59: 1351 1.59 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 3203 Sorted by residual: bond pdb=" C3 UEG A 501 " pdb=" O3 UEG A 501 " ideal model delta sigma weight residual 1.348 1.401 -0.053 2.00e-02 2.50e+03 7.12e+00 bond pdb=" N ARG A 429 " pdb=" CA ARG A 429 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.33e-02 5.65e+03 5.57e+00 bond pdb=" C4 UEG A 501 " pdb=" C5 UEG A 501 " ideal model delta sigma weight residual 1.399 1.355 0.044 2.00e-02 2.50e+03 4.81e+00 bond pdb=" C3 UEG A 501 " pdb=" C4 UEG A 501 " ideal model delta sigma weight residual 1.392 1.354 0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C2 UEG A 501 " pdb=" N1 UEG A 501 " ideal model delta sigma weight residual 1.322 1.352 -0.030 2.00e-02 2.50e+03 2.18e+00 ... (remaining 3198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 4329 2.37 - 4.74: 41 4.74 - 7.11: 6 7.11 - 9.48: 1 9.48 - 11.86: 1 Bond angle restraints: 4378 Sorted by residual: angle pdb=" CB MET A 455 " pdb=" CG MET A 455 " pdb=" SD MET A 455 " ideal model delta sigma weight residual 112.70 124.56 -11.86 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CA TYR A 280 " pdb=" CB TYR A 280 " pdb=" CG TYR A 280 " ideal model delta sigma weight residual 113.90 119.08 -5.18 1.80e+00 3.09e-01 8.27e+00 angle pdb=" CA LYS A 276 " pdb=" CB LYS A 276 " pdb=" CG LYS A 276 " ideal model delta sigma weight residual 114.10 119.21 -5.11 2.00e+00 2.50e-01 6.54e+00 angle pdb=" N ARG A 429 " pdb=" CA ARG A 429 " pdb=" C ARG A 429 " ideal model delta sigma weight residual 112.54 109.54 3.00 1.22e+00 6.72e-01 6.06e+00 angle pdb=" CB MET A 106 " pdb=" CG MET A 106 " pdb=" SD MET A 106 " ideal model delta sigma weight residual 112.70 119.93 -7.23 3.00e+00 1.11e-01 5.81e+00 ... (remaining 4373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 1533 16.92 - 33.83: 212 33.83 - 50.75: 53 50.75 - 67.67: 8 67.67 - 84.58: 4 Dihedral angle restraints: 1810 sinusoidal: 661 harmonic: 1149 Sorted by residual: dihedral pdb=" CG ARG A 429 " pdb=" CD ARG A 429 " pdb=" NE ARG A 429 " pdb=" CZ ARG A 429 " ideal model delta sinusoidal sigma weight residual -90.00 -34.77 -55.23 2 1.50e+01 4.44e-03 1.44e+01 dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N TYR A 79 " pdb=" CA TYR A 79 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" N LEU A 67 " pdb=" CA LEU A 67 " pdb=" CB LEU A 67 " pdb=" CG LEU A 67 " ideal model delta sinusoidal sigma weight residual -60.00 -115.48 55.48 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 1807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 300 0.028 - 0.056: 115 0.056 - 0.085: 62 0.085 - 0.113: 24 0.113 - 0.141: 4 Chirality restraints: 505 Sorted by residual: chirality pdb=" CB ILE A 175 " pdb=" CA ILE A 175 " pdb=" CG1 ILE A 175 " pdb=" CG2 ILE A 175 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ASN A 399 " pdb=" N ASN A 399 " pdb=" C ASN A 399 " pdb=" CB ASN A 399 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL A 400 " pdb=" N VAL A 400 " pdb=" C VAL A 400 " pdb=" CB VAL A 400 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 502 not shown) Planarity restraints: 524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 36 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.06e+00 pdb=" N PRO A 37 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 37 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 37 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 141 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C GLY A 141 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY A 141 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR A 142 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 143 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" C CYS A 143 " -0.034 2.00e-02 2.50e+03 pdb=" O CYS A 143 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 144 " 0.012 2.00e-02 2.50e+03 ... (remaining 521 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 384 2.75 - 3.28: 3392 3.28 - 3.82: 5604 3.82 - 4.36: 6269 4.36 - 4.90: 10810 Nonbonded interactions: 26459 Sorted by model distance: nonbonded pdb=" OD1 ASN A 356 " pdb=" OG SER A 382 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR A 289 " pdb=" OH TYR A 383 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR A 273 " pdb=" OD1 ASN A 410 " model vdw 2.262 3.040 nonbonded pdb=" O ALA A 49 " pdb=" ND2 ASN A 53 " model vdw 2.265 3.120 nonbonded pdb=" O VAL A 70 " pdb=" OG1 THR A 74 " model vdw 2.267 3.040 ... (remaining 26454 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.190 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3203 Z= 0.230 Angle : 0.622 11.855 4378 Z= 0.325 Chirality : 0.041 0.141 505 Planarity : 0.006 0.050 524 Dihedral : 16.891 84.584 1076 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.60 % Allowed : 26.13 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.43), residues: 383 helix: 0.39 (0.29), residues: 305 sheet: None (None), residues: 0 loop : 0.46 (0.80), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.012 0.001 PHE A 71 TYR 0.013 0.001 TYR A 383 ARG 0.003 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7862 (mm110) outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.1874 time to fit residues: 11.9523 Evaluate side-chains 50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 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 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.142181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112966 restraints weight = 3516.224| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.75 r_work: 0.3058 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3203 Z= 0.247 Angle : 0.613 6.977 4378 Z= 0.321 Chirality : 0.043 0.207 505 Planarity : 0.005 0.042 524 Dihedral : 6.067 81.143 427 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.10 % Allowed : 24.02 % Favored : 73.87 % 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: 1.50 (0.44), residues: 383 helix: 1.09 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 1.07 (0.89), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 94 HIS 0.001 0.000 HIS A 135 PHE 0.016 0.001 PHE A 439 TYR 0.013 0.002 TYR A 383 ARG 0.002 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASN cc_start: 0.7690 (p0) cc_final: 0.7398 (p0) outliers start: 7 outliers final: 2 residues processed: 60 average time/residue: 0.1286 time to fit residues: 9.7839 Evaluate side-chains 51 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 423 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.2980 chunk 27 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.0010 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.143723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.114927 restraints weight = 3443.392| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.72 r_work: 0.3099 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3203 Z= 0.203 Angle : 0.588 6.294 4378 Z= 0.304 Chirality : 0.043 0.191 505 Planarity : 0.004 0.044 524 Dihedral : 5.527 76.609 425 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.80 % Allowed : 26.13 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.44), residues: 383 helix: 1.25 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 1.00 (0.90), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.015 0.001 PHE A 439 TYR 0.014 0.001 TYR A 383 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8526 (tmm) cc_final: 0.7945 (tmm) REVERT: A 32 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7816 (mm-30) REVERT: A 368 ASN cc_start: 0.7582 (p0) cc_final: 0.7303 (p0) outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 0.1306 time to fit residues: 9.4303 Evaluate side-chains 52 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 130 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 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 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.143382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.113740 restraints weight = 3518.658| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.81 r_work: 0.3032 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3203 Z= 0.255 Angle : 0.608 8.391 4378 Z= 0.316 Chirality : 0.044 0.219 505 Planarity : 0.004 0.046 524 Dihedral : 5.507 74.197 425 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.20 % Allowed : 23.72 % Favored : 72.07 % 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 (0.43), residues: 383 helix: 1.25 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.83 (0.90), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.017 0.001 PHE A 439 TYR 0.015 0.002 TYR A 383 ARG 0.001 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 368 ASN cc_start: 0.7671 (p0) cc_final: 0.7393 (p0) REVERT: A 458 MET cc_start: 0.7667 (tpt) cc_final: 0.7248 (ptp) outliers start: 14 outliers final: 7 residues processed: 61 average time/residue: 0.1153 time to fit residues: 9.1670 Evaluate side-chains 56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 423 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.0000 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.142549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.113522 restraints weight = 3496.988| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.76 r_work: 0.3051 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3203 Z= 0.195 Angle : 0.587 11.372 4378 Z= 0.296 Chirality : 0.042 0.213 505 Planarity : 0.004 0.045 524 Dihedral : 5.275 70.096 425 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.00 % Allowed : 25.53 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.43), residues: 383 helix: 1.32 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.74 (0.89), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.014 0.001 PHE A 439 TYR 0.015 0.001 TYR A 383 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8663 (mt) cc_final: 0.8372 (mp) REVERT: A 368 ASN cc_start: 0.7396 (p0) cc_final: 0.7125 (p0) REVERT: A 458 MET cc_start: 0.7601 (tpt) cc_final: 0.7203 (ptp) outliers start: 10 outliers final: 6 residues processed: 62 average time/residue: 0.1166 time to fit residues: 9.4624 Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.0970 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.148772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.119700 restraints weight = 3474.294| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.81 r_work: 0.3113 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3203 Z= 0.189 Angle : 0.589 11.441 4378 Z= 0.294 Chirality : 0.042 0.212 505 Planarity : 0.004 0.044 524 Dihedral : 4.999 61.072 425 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.00 % Allowed : 25.83 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.43), residues: 383 helix: 1.43 (0.29), residues: 318 sheet: None (None), residues: 0 loop : 0.61 (0.85), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.012 0.001 PHE A 71 TYR 0.015 0.001 TYR A 383 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8715 (mt) cc_final: 0.8425 (mp) REVERT: A 368 ASN cc_start: 0.7464 (p0) cc_final: 0.7188 (p0) REVERT: A 458 MET cc_start: 0.7539 (tpt) cc_final: 0.7206 (ptp) outliers start: 10 outliers final: 7 residues processed: 57 average time/residue: 0.1080 time to fit residues: 8.0681 Evaluate side-chains 56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 416 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.136979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.108515 restraints weight = 3591.091| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.70 r_work: 0.3029 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3203 Z= 0.239 Angle : 0.613 10.151 4378 Z= 0.308 Chirality : 0.043 0.218 505 Planarity : 0.004 0.044 524 Dihedral : 4.843 53.384 425 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.40 % Allowed : 26.43 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.43), residues: 383 helix: 1.41 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.77 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.014 0.001 PHE A 71 TYR 0.015 0.001 TYR A 383 ARG 0.000 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8629 (mt) cc_final: 0.8320 (mp) REVERT: A 368 ASN cc_start: 0.7348 (p0) cc_final: 0.7093 (p0) REVERT: A 458 MET cc_start: 0.7482 (tpt) cc_final: 0.7119 (ptp) outliers start: 8 outliers final: 7 residues processed: 60 average time/residue: 0.1280 time to fit residues: 9.7214 Evaluate side-chains 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 416 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.144822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.116516 restraints weight = 3481.299| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.71 r_work: 0.3045 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3203 Z= 0.237 Angle : 0.622 9.216 4378 Z= 0.310 Chirality : 0.043 0.222 505 Planarity : 0.004 0.045 524 Dihedral : 4.602 42.033 425 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.60 % Allowed : 24.62 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.43), residues: 383 helix: 1.40 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.70 (0.87), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.014 0.001 PHE A 71 TYR 0.015 0.001 TYR A 383 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8685 (mt) cc_final: 0.8382 (mp) REVERT: A 458 MET cc_start: 0.7477 (tpt) cc_final: 0.7128 (ptp) outliers start: 12 outliers final: 9 residues processed: 60 average time/residue: 0.1380 time to fit residues: 10.3628 Evaluate side-chains 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 416 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.133448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.107148 restraints weight = 3615.655| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.45 r_work: 0.2946 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3203 Z= 0.253 Angle : 0.629 8.665 4378 Z= 0.316 Chirality : 0.044 0.233 505 Planarity : 0.004 0.045 524 Dihedral : 4.457 33.021 425 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.40 % Allowed : 25.83 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.43), residues: 383 helix: 1.38 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.68 (0.87), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.015 0.001 PHE A 71 TYR 0.014 0.002 TYR A 383 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8787 (mt) cc_final: 0.8472 (mp) outliers start: 8 outliers final: 8 residues processed: 55 average time/residue: 0.1365 time to fit residues: 9.5064 Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.133362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.107060 restraints weight = 3550.538| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.44 r_work: 0.2958 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3203 Z= 0.256 Angle : 0.633 8.754 4378 Z= 0.318 Chirality : 0.044 0.237 505 Planarity : 0.004 0.046 524 Dihedral : 4.403 28.207 425 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.30 % Allowed : 24.92 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.43), residues: 383 helix: 1.32 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 0.60 (0.86), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.015 0.001 PHE A 71 TYR 0.015 0.002 TYR A 383 ARG 0.000 0.000 ARG A 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8781 (mt) cc_final: 0.8469 (mp) REVERT: A 455 MET cc_start: 0.8148 (mmm) cc_final: 0.7634 (mtm) outliers start: 11 outliers final: 10 residues processed: 56 average time/residue: 0.1344 time to fit residues: 9.5076 Evaluate side-chains 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 32 optimal weight: 0.0570 chunk 7 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.137957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.111825 restraints weight = 3570.284| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.41 r_work: 0.3063 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3203 Z= 0.201 Angle : 0.628 9.798 4378 Z= 0.310 Chirality : 0.043 0.234 505 Planarity : 0.004 0.046 524 Dihedral : 4.266 20.069 425 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.00 % Allowed : 25.83 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.43), residues: 383 helix: 1.35 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.73 (0.88), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.011 0.001 PHE A 71 TYR 0.015 0.001 TYR A 383 ARG 0.001 0.000 ARG A 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1754.95 seconds wall clock time: 31 minutes 58.46 seconds (1918.46 seconds total)