Starting phenix.real_space_refine on Wed Sep 17 03:24:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7t_39827/09_2025/8z7t_39827.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7t_39827/09_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_39827/09_2025/8z7t_39827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7t_39827/09_2025/8z7t_39827.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7t_39827/09_2025/8z7t_39827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7t_39827/09_2025/8z7t_39827.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.18, per 1000 atoms: 0.38 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: 0.35 Conformation dependent library (CDL) restraints added in 142.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.10 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: 0.53 Time building geometry restraints manager: 0.45 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: 1.490 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.670 Find NCS groups from input model: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.400 ------------------------------------------------------------------------------- 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= 0.176 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 : 10.40 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 429 TYR 0.013 0.001 TYR A 383 PHE 0.012 0.001 PHE A 71 TRP 0.011 0.001 TRP A 94 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 3203) covalent geometry : angle 0.62216 ( 4378) hydrogen bonds : bond 0.18290 ( 245) hydrogen bonds : angle 7.18642 ( 735) *********************** 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 : 0.112 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: 0.0812 time to fit residues: 5.1640 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 : 0.117 ------------------------------------------------------------------------------- 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 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.137551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.110929 restraints weight = 3561.015| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.43 r_work: 0.3011 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1360 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= 0.156 Angle : 0.602 7.010 4378 Z= 0.314 Chirality : 0.043 0.193 505 Planarity : 0.005 0.041 524 Dihedral : 6.039 80.885 427 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.50 % Allowed : 24.02 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.44), residues: 383 helix: 1.14 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 1.08 (0.89), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 429 TYR 0.013 0.002 TYR A 383 PHE 0.015 0.001 PHE A 439 TRP 0.016 0.002 TRP A 284 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3203) covalent geometry : angle 0.60219 ( 4378) hydrogen bonds : bond 0.05180 ( 245) hydrogen bonds : angle 4.56558 ( 735) *********************** 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 59 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7803 (mm-30) REVERT: A 368 ASN cc_start: 0.7745 (p0) cc_final: 0.7470 (p0) outliers start: 5 outliers final: 0 residues processed: 59 average time/residue: 0.0503 time to fit residues: 3.8211 Evaluate side-chains 50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3543 r_free = 0.3543 target = 0.141285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.112161 restraints weight = 3549.700| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.75 r_work: 0.3080 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3203 Z= 0.161 Angle : 0.587 5.856 4378 Z= 0.307 Chirality : 0.043 0.203 505 Planarity : 0.004 0.045 524 Dihedral : 5.505 74.784 425 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.70 % Allowed : 24.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.44), residues: 383 helix: 1.21 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 1.12 (0.89), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 277 TYR 0.014 0.002 TYR A 383 PHE 0.016 0.001 PHE A 439 TRP 0.016 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 3203) covalent geometry : angle 0.58727 ( 4378) hydrogen bonds : bond 0.04969 ( 245) hydrogen bonds : angle 4.31916 ( 735) *********************** 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 62 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASN cc_start: 0.7633 (p0) cc_final: 0.7347 (p0) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 0.0579 time to fit residues: 4.3791 Evaluate side-chains 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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 423 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.143741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.115077 restraints weight = 3466.383| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.74 r_work: 0.3029 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3203 Z= 0.168 Angle : 0.612 10.073 4378 Z= 0.316 Chirality : 0.044 0.211 505 Planarity : 0.004 0.046 524 Dihedral : 5.644 78.693 425 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.20 % Allowed : 24.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.43), residues: 383 helix: 1.23 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.83 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 402 TYR 0.014 0.002 TYR A 383 PHE 0.017 0.001 PHE A 439 TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 3203) covalent geometry : angle 0.61169 ( 4378) hydrogen bonds : bond 0.04925 ( 245) hydrogen bonds : angle 4.27303 ( 735) *********************** 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 64 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.8458 (tmm) cc_final: 0.7905 (tmm) REVERT: A 368 ASN cc_start: 0.7578 (p0) cc_final: 0.7311 (p0) REVERT: A 458 MET cc_start: 0.7655 (tpt) cc_final: 0.7181 (ptp) outliers start: 14 outliers final: 6 residues processed: 62 average time/residue: 0.0503 time to fit residues: 4.0733 Evaluate side-chains 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 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 = 0.3426 r_free = 0.3426 target = 0.133570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.106979 restraints weight = 3625.208| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.47 r_work: 0.2979 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3203 Z= 0.155 Angle : 0.603 11.149 4378 Z= 0.306 Chirality : 0.043 0.207 505 Planarity : 0.004 0.046 524 Dihedral : 5.449 73.681 425 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.30 % Allowed : 24.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.43), residues: 383 helix: 1.26 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.81 (0.89), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 277 TYR 0.015 0.001 TYR A 383 PHE 0.015 0.001 PHE A 439 TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 3203) covalent geometry : angle 0.60348 ( 4378) hydrogen bonds : bond 0.04738 ( 245) hydrogen bonds : angle 4.20274 ( 735) *********************** 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 61 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8750 (mt) cc_final: 0.8458 (mp) REVERT: A 368 ASN cc_start: 0.7461 (p0) cc_final: 0.7169 (p0) REVERT: A 458 MET cc_start: 0.7553 (tpt) cc_final: 0.7268 (ptp) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 0.0477 time to fit residues: 3.6417 Evaluate side-chains 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 416 VAL Chi-restraints excluded: chain A residue 423 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.132264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.105595 restraints weight = 3639.476| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.49 r_work: 0.2984 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3203 Z= 0.164 Angle : 0.614 11.089 4378 Z= 0.311 Chirality : 0.043 0.218 505 Planarity : 0.004 0.046 524 Dihedral : 5.438 72.108 425 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.60 % Allowed : 24.02 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.43), residues: 383 helix: 1.26 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.78 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 456 TYR 0.015 0.002 TYR A 383 PHE 0.015 0.001 PHE A 439 TRP 0.017 0.002 TRP A 94 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3203) covalent geometry : angle 0.61371 ( 4378) hydrogen bonds : bond 0.04801 ( 245) hydrogen bonds : angle 4.21199 ( 735) *********************** 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 63 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8802 (mt) cc_final: 0.8495 (mp) REVERT: A 368 ASN cc_start: 0.7493 (p0) cc_final: 0.7192 (p0) REVERT: A 458 MET cc_start: 0.7486 (tpt) cc_final: 0.7267 (ptp) outliers start: 12 outliers final: 9 residues processed: 61 average time/residue: 0.0487 time to fit residues: 3.9192 Evaluate side-chains 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 28 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.145726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.116706 restraints weight = 3521.199| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.81 r_work: 0.3056 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3203 Z= 0.147 Angle : 0.613 10.048 4378 Z= 0.305 Chirality : 0.043 0.222 505 Planarity : 0.004 0.046 524 Dihedral : 5.051 60.401 425 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.30 % Allowed : 24.32 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.43), residues: 383 helix: 1.37 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.84 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 277 TYR 0.016 0.001 TYR A 383 PHE 0.014 0.001 PHE A 439 TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 3203) covalent geometry : angle 0.61324 ( 4378) hydrogen bonds : bond 0.04585 ( 245) hydrogen bonds : angle 4.11658 ( 735) *********************** 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 61 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8754 (mt) cc_final: 0.8458 (mp) REVERT: A 458 MET cc_start: 0.7496 (tpt) cc_final: 0.7155 (ptp) outliers start: 11 outliers final: 9 residues processed: 59 average time/residue: 0.0510 time to fit residues: 3.9733 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 : 0.108 ------------------------------------------------------------------------------- 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 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 19 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.136587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.108077 restraints weight = 3670.461| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.68 r_work: 0.3062 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3203 Z= 0.152 Angle : 0.621 9.342 4378 Z= 0.309 Chirality : 0.043 0.223 505 Planarity : 0.004 0.045 524 Dihedral : 4.760 48.696 425 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.70 % Allowed : 26.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.43), residues: 383 helix: 1.36 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.83 (0.89), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 277 TYR 0.016 0.001 TYR A 383 PHE 0.013 0.001 PHE A 71 TRP 0.028 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3203) covalent geometry : angle 0.62082 ( 4378) hydrogen bonds : bond 0.04635 ( 245) hydrogen bonds : angle 4.15081 ( 735) *********************** 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 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8677 (mt) cc_final: 0.8376 (mp) REVERT: A 458 MET cc_start: 0.7480 (tpt) cc_final: 0.7113 (ptp) outliers start: 9 outliers final: 8 residues processed: 56 average time/residue: 0.0494 time to fit residues: 3.6131 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 : 0.075 ------------------------------------------------------------------------------- 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 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 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 = 0.3462 r_free = 0.3462 target = 0.134914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.106467 restraints weight = 3644.784| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.67 r_work: 0.3015 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2402 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= 0.157 Angle : 0.625 9.078 4378 Z= 0.312 Chirality : 0.044 0.231 505 Planarity : 0.004 0.045 524 Dihedral : 4.554 38.672 425 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.30 % Allowed : 25.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.43), residues: 383 helix: 1.37 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.84 (0.89), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 277 TYR 0.015 0.001 TYR A 383 PHE 0.013 0.001 PHE A 71 TRP 0.027 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 3203) covalent geometry : angle 0.62508 ( 4378) hydrogen bonds : bond 0.04659 ( 245) hydrogen bonds : angle 4.16007 ( 735) *********************** 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 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8659 (mt) cc_final: 0.8346 (mp) REVERT: A 458 MET cc_start: 0.7464 (tpt) cc_final: 0.7137 (ptp) outliers start: 11 outliers final: 10 residues processed: 56 average time/residue: 0.0489 time to fit residues: 3.6269 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 : 0.135 ------------------------------------------------------------------------------- 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 162 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.133521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.107009 restraints weight = 3610.278| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.47 r_work: 0.2959 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3203 Z= 0.154 Angle : 0.625 8.884 4378 Z= 0.311 Chirality : 0.044 0.237 505 Planarity : 0.004 0.046 524 Dihedral : 4.368 28.221 425 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.00 % Allowed : 26.13 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.43), residues: 383 helix: 1.39 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.81 (0.90), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 456 TYR 0.015 0.001 TYR A 383 PHE 0.013 0.001 PHE A 71 TRP 0.025 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3203) covalent geometry : angle 0.62494 ( 4378) hydrogen bonds : bond 0.04603 ( 245) hydrogen bonds : angle 4.15010 ( 735) ********************** 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 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.064 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8762 (mt) cc_final: 0.8454 (mp) outliers start: 10 outliers final: 9 residues processed: 55 average time/residue: 0.0501 time to fit residues: 3.6142 Evaluate side-chains 56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 162 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.135095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.107727 restraints weight = 3647.292| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.54 r_work: 0.2979 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3203 Z= 0.149 Angle : 0.623 9.037 4378 Z= 0.310 Chirality : 0.043 0.233 505 Planarity : 0.004 0.045 524 Dihedral : 4.297 23.101 425 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 : 26.73 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.43), residues: 383 helix: 1.39 (0.28), residues: 319 sheet: None (None), residues: 0 loop : 0.81 (0.90), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 456 TYR 0.016 0.001 TYR A 383 PHE 0.013 0.001 PHE A 71 TRP 0.025 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3203) covalent geometry : angle 0.62310 ( 4378) hydrogen bonds : bond 0.04555 ( 245) hydrogen bonds : angle 4.14480 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 911.05 seconds wall clock time: 16 minutes 20.90 seconds (980.90 seconds total)