Starting phenix.real_space_refine on Fri Aug 22 15:14:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jwh_36683/08_2025/8jwh_36683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jwh_36683/08_2025/8jwh_36683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jwh_36683/08_2025/8jwh_36683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jwh_36683/08_2025/8jwh_36683.map" model { file = "/net/cci-nas-00/data/ceres_data/8jwh_36683/08_2025/8jwh_36683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jwh_36683/08_2025/8jwh_36683.cif" } resolution = 3.34 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= 0.000 sd= 0.003 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 29 5.16 5 C 3115 2.51 5 N 806 2.21 5 O 920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Time building chain proxies: 1.07, per 1000 atoms: 0.22 Number of scatterers: 4870 At special positions: 0 Unit cell: (77.0408, 84.5774, 69.5042, 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 29 16.00 O 920 8.00 N 806 7.00 C 3115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 512 " - pdb=" SG CYS A 524 " distance=2.03 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: 0.47 Conformation dependent library (CDL) restraints added in 194.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 3 sheets defined 70.7% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 2 through 35 Processing helix chain 'A' and resid 37 through 64 removed outlier: 3.584A pdb=" N VAL A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 70 removed outlier: 4.100A pdb=" N GLU A 69 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.635A pdb=" N LEU A 90 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 112 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 139 through 176 removed outlier: 4.530A pdb=" N LYS A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLN A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 180 through 188 Processing helix chain 'A' and resid 201 through 234 Proline residue: A 217 - end of helix Processing helix chain 'A' and resid 260 through 265 Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 285 through 300 Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 347 through 367 removed outlier: 3.645A pdb=" N TYR A 367 " --> pdb=" O TYR A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 379 through 395 Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 413 through 448 Proline residue: A 433 - end of helix Processing helix chain 'A' and resid 453 through 466 removed outlier: 4.404A pdb=" N LYS A 457 " --> pdb=" O ASP A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 484 Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.987A pdb=" N TYR A 498 " --> pdb=" O PHE A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.519A pdb=" N LYS A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 543 removed outlier: 4.036A pdb=" N GLY A 543 " --> pdb=" O MET A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 563 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 245 removed outlier: 6.211A pdb=" N LEU A 244 " --> pdb=" O VAL A 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 332 297 hydrogen bonds defined for protein. 864 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: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1569 1.34 - 1.46: 1197 1.46 - 1.58: 2190 1.58 - 1.70: 1 1.70 - 1.81: 50 Bond restraints: 5007 Sorted by residual: bond pdb=" C GLU A 127 " pdb=" N PRO A 128 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.53e+00 bond pdb=" CB PRO A 66 " pdb=" CG PRO A 66 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.16e+00 bond pdb=" C ASN A 116 " pdb=" N PRO A 117 " ideal model delta sigma weight residual 1.332 1.350 -0.017 8.90e-03 1.26e+04 3.73e+00 bond pdb=" C GLU A 571 " pdb=" N PRO A 572 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.55e+00 bond pdb=" C LYS A 216 " pdb=" N PRO A 217 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.38e-02 5.25e+03 3.05e+00 ... (remaining 5002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 6437 1.66 - 3.32: 301 3.32 - 4.98: 45 4.98 - 6.63: 13 6.63 - 8.29: 7 Bond angle restraints: 6803 Sorted by residual: angle pdb=" CA PRO A 66 " pdb=" N PRO A 66 " pdb=" CD PRO A 66 " ideal model delta sigma weight residual 112.00 103.71 8.29 1.40e+00 5.10e-01 3.51e+01 angle pdb=" N VAL A 275 " pdb=" CA VAL A 275 " pdb=" C VAL A 275 " ideal model delta sigma weight residual 106.21 112.43 -6.22 1.07e+00 8.73e-01 3.38e+01 angle pdb=" N ASN A 119 " pdb=" CA ASN A 119 " pdb=" C ASN A 119 " ideal model delta sigma weight residual 108.69 101.49 7.20 1.80e+00 3.09e-01 1.60e+01 angle pdb=" N VAL A 300 " pdb=" CA VAL A 300 " pdb=" C VAL A 300 " ideal model delta sigma weight residual 112.98 108.45 4.53 1.25e+00 6.40e-01 1.31e+01 angle pdb=" C ASN A 119 " pdb=" CA ASN A 119 " pdb=" CB ASN A 119 " ideal model delta sigma weight residual 110.17 113.61 -3.44 9.90e-01 1.02e+00 1.21e+01 ... (remaining 6798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 2455 17.96 - 35.92: 362 35.92 - 53.88: 111 53.88 - 71.84: 19 71.84 - 89.80: 12 Dihedral angle restraints: 2959 sinusoidal: 1205 harmonic: 1754 Sorted by residual: dihedral pdb=" CA ASN A 119 " pdb=" C ASN A 119 " pdb=" N PRO A 120 " pdb=" CA PRO A 120 " ideal model delta harmonic sigma weight residual -180.00 -146.08 -33.92 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA GLU A 127 " pdb=" C GLU A 127 " pdb=" N PRO A 128 " pdb=" CA PRO A 128 " ideal model delta harmonic sigma weight residual 180.00 -154.24 -25.76 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA GLN A 121 " pdb=" C GLN A 121 " pdb=" N GLU A 122 " pdb=" CA GLU A 122 " ideal model delta harmonic sigma weight residual -180.00 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 2956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 442 0.035 - 0.071: 185 0.071 - 0.106: 62 0.106 - 0.141: 17 0.141 - 0.176: 4 Chirality restraints: 710 Sorted by residual: chirality pdb=" CA PRO A 120 " pdb=" N PRO A 120 " pdb=" C PRO A 120 " pdb=" CB PRO A 120 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA PRO A 240 " pdb=" N PRO A 240 " pdb=" C PRO A 240 " pdb=" CB PRO A 240 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" CB THR A 107 " pdb=" CA THR A 107 " pdb=" OG1 THR A 107 " pdb=" CG2 THR A 107 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.80e-01 ... (remaining 707 not shown) Planarity restraints: 881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 65 " -0.090 5.00e-02 4.00e+02 1.31e-01 2.73e+01 pdb=" N PRO A 66 " 0.226 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 116 " -0.054 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO A 117 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 481 " 0.044 5.00e-02 4.00e+02 6.69e-02 7.15e+00 pdb=" N PRO A 482 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 482 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 482 " 0.037 5.00e-02 4.00e+02 ... (remaining 878 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 117 2.69 - 3.24: 5058 3.24 - 3.79: 8284 3.79 - 4.35: 10541 4.35 - 4.90: 17198 Nonbonded interactions: 41198 Sorted by model distance: nonbonded pdb=" OH TYR A 219 " pdb=" O VAL A 467 " model vdw 2.135 3.040 nonbonded pdb=" OE1 GLU A 209 " pdb=" OH TYR A 436 " model vdw 2.187 3.040 nonbonded pdb=" O THR A 107 " pdb=" OG1 THR A 111 " model vdw 2.193 3.040 nonbonded pdb=" O ALA A 483 " pdb=" OG SER A 489 " model vdw 2.211 3.040 nonbonded pdb=" OG SER A 152 " pdb=" OE1 GLU A 153 " model vdw 2.235 3.040 ... (remaining 41193 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: 0.780 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.030 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 0.004 0.114 5010 Z= 0.193 Angle : 0.839 8.292 6809 Z= 0.504 Chirality : 0.045 0.176 710 Planarity : 0.008 0.131 881 Dihedral : 19.175 89.805 1820 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.76 % Allowed : 28.65 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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 (0.34), residues: 595 helix: 0.30 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -1.27 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 500 TYR 0.014 0.002 TYR A 367 PHE 0.012 0.002 PHE A 420 TRP 0.024 0.002 TRP A 455 HIS 0.006 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 5007) covalent geometry : angle 0.83967 ( 6803) SS BOND : bond 0.00197 ( 3) SS BOND : angle 0.57465 ( 6) hydrogen bonds : bond 0.14451 ( 297) hydrogen bonds : angle 6.89555 ( 864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6511 (mm-30) REVERT: A 220 GLU cc_start: 0.6823 (tt0) cc_final: 0.6455 (tt0) outliers start: 4 outliers final: 0 residues processed: 83 average time/residue: 0.0606 time to fit residues: 6.9387 Evaluate side-chains 72 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.173341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.148292 restraints weight = 7562.194| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.70 r_work: 0.3822 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5010 Z= 0.158 Angle : 0.683 8.334 6809 Z= 0.351 Chirality : 0.044 0.159 710 Planarity : 0.006 0.082 881 Dihedral : 5.637 33.308 642 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.17 % Allowed : 26.38 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.18 (0.33), residues: 595 helix: 0.47 (0.25), residues: 397 sheet: -4.38 (1.23), residues: 10 loop : -0.95 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 143 TYR 0.016 0.002 TYR A 367 PHE 0.012 0.002 PHE A 351 TRP 0.012 0.001 TRP A 455 HIS 0.005 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5007) covalent geometry : angle 0.68275 ( 6803) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.49262 ( 6) hydrogen bonds : bond 0.05969 ( 297) hydrogen bonds : angle 5.33783 ( 864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6606 (mm-30) REVERT: A 220 GLU cc_start: 0.7050 (tt0) cc_final: 0.6736 (tt0) REVERT: A 539 MET cc_start: 0.7419 (tmm) cc_final: 0.7081 (tmm) outliers start: 22 outliers final: 8 residues processed: 99 average time/residue: 0.0617 time to fit residues: 8.2049 Evaluate side-chains 74 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 444 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 7 optimal weight: 0.0060 chunk 53 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** 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 = 0.4256 r_free = 0.4256 target = 0.173805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.149061 restraints weight = 7487.831| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.65 r_work: 0.3818 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5010 Z= 0.149 Angle : 0.654 7.959 6809 Z= 0.334 Chirality : 0.043 0.149 710 Planarity : 0.006 0.069 881 Dihedral : 5.382 31.821 642 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.66 % Allowed : 27.70 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.01 (0.34), residues: 595 helix: 0.58 (0.25), residues: 397 sheet: -4.25 (1.27), residues: 10 loop : -0.85 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.015 0.001 TYR A 497 PHE 0.012 0.001 PHE A 351 TRP 0.010 0.001 TRP A 548 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5007) covalent geometry : angle 0.65469 ( 6803) SS BOND : bond 0.00157 ( 3) SS BOND : angle 0.31393 ( 6) hydrogen bonds : bond 0.05716 ( 297) hydrogen bonds : angle 5.12407 ( 864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7593 (mm-30) cc_final: 0.6982 (mm-30) REVERT: A 332 ASP cc_start: 0.7379 (m-30) cc_final: 0.7170 (m-30) REVERT: A 539 MET cc_start: 0.7436 (tmm) cc_final: 0.7140 (tmm) outliers start: 14 outliers final: 11 residues processed: 89 average time/residue: 0.0456 time to fit residues: 5.7806 Evaluate side-chains 77 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 493 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** 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 = 0.4230 r_free = 0.4230 target = 0.171545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.146620 restraints weight = 7509.973| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.68 r_work: 0.3798 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5010 Z= 0.154 Angle : 0.657 8.434 6809 Z= 0.332 Chirality : 0.043 0.151 710 Planarity : 0.005 0.061 881 Dihedral : 5.236 30.041 642 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.36 % Allowed : 28.27 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.08 (0.34), residues: 595 helix: 0.63 (0.25), residues: 398 sheet: -4.12 (1.22), residues: 10 loop : -0.78 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.015 0.002 TYR A 497 PHE 0.014 0.001 PHE A 351 TRP 0.010 0.001 TRP A 548 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5007) covalent geometry : angle 0.65702 ( 6803) SS BOND : bond 0.00205 ( 3) SS BOND : angle 0.36545 ( 6) hydrogen bonds : bond 0.05661 ( 297) hydrogen bonds : angle 5.04346 ( 864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7156 (mm-30) REVERT: A 333 LEU cc_start: 0.7740 (mt) cc_final: 0.7490 (mt) REVERT: A 539 MET cc_start: 0.7373 (tmm) cc_final: 0.7114 (tmm) outliers start: 23 outliers final: 14 residues processed: 95 average time/residue: 0.0399 time to fit residues: 5.5708 Evaluate side-chains 81 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 444 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.172558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.147324 restraints weight = 7638.993| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.72 r_work: 0.3798 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5010 Z= 0.147 Angle : 0.641 8.974 6809 Z= 0.325 Chirality : 0.042 0.151 710 Planarity : 0.005 0.056 881 Dihedral : 5.101 29.453 642 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.55 % Allowed : 27.70 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.23 (0.34), residues: 595 helix: 0.72 (0.25), residues: 398 sheet: -4.03 (1.27), residues: 10 loop : -0.65 (0.49), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 500 TYR 0.015 0.002 TYR A 497 PHE 0.013 0.001 PHE A 351 TRP 0.010 0.001 TRP A 548 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5007) covalent geometry : angle 0.64078 ( 6803) SS BOND : bond 0.00217 ( 3) SS BOND : angle 0.41441 ( 6) hydrogen bonds : bond 0.05545 ( 297) hydrogen bonds : angle 4.98813 ( 864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.131 Fit side-chains REVERT: A 96 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.6928 (mmmt) REVERT: A 149 SER cc_start: 0.8695 (p) cc_final: 0.8096 (t) REVERT: A 333 LEU cc_start: 0.7630 (mt) cc_final: 0.7352 (mt) REVERT: A 390 MET cc_start: 0.7733 (mmm) cc_final: 0.7412 (mmm) REVERT: A 507 PHE cc_start: 0.8730 (m-10) cc_final: 0.8529 (m-10) REVERT: A 539 MET cc_start: 0.7413 (tmm) cc_final: 0.7169 (tmm) REVERT: A 592 TRP cc_start: 0.3744 (OUTLIER) cc_final: 0.2276 (m100) outliers start: 24 outliers final: 15 residues processed: 90 average time/residue: 0.0491 time to fit residues: 6.2382 Evaluate side-chains 82 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 592 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 0.0770 chunk 5 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.173459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.148443 restraints weight = 7675.674| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.72 r_work: 0.3811 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5010 Z= 0.141 Angle : 0.645 8.663 6809 Z= 0.327 Chirality : 0.043 0.197 710 Planarity : 0.005 0.056 881 Dihedral : 5.037 29.360 642 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.17 % Allowed : 28.65 % Favored : 67.17 % 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: 0.28 (0.34), residues: 595 helix: 0.75 (0.25), residues: 398 sheet: -4.15 (1.27), residues: 10 loop : -0.61 (0.50), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 500 TYR 0.014 0.001 TYR A 497 PHE 0.012 0.001 PHE A 351 TRP 0.009 0.001 TRP A 548 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5007) covalent geometry : angle 0.64493 ( 6803) SS BOND : bond 0.00175 ( 3) SS BOND : angle 0.37849 ( 6) hydrogen bonds : bond 0.05404 ( 297) hydrogen bonds : angle 4.92075 ( 864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.144 Fit side-chains REVERT: A 96 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7106 (mmmt) REVERT: A 390 MET cc_start: 0.7840 (mmm) cc_final: 0.7417 (mmm) REVERT: A 456 MET cc_start: 0.8103 (mmp) cc_final: 0.7170 (mmt) REVERT: A 592 TRP cc_start: 0.3700 (OUTLIER) cc_final: 0.2416 (m100) outliers start: 22 outliers final: 15 residues processed: 88 average time/residue: 0.0577 time to fit residues: 6.9345 Evaluate side-chains 79 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 592 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 1 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.165413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.139747 restraints weight = 7660.185| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.67 r_work: 0.3699 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5010 Z= 0.221 Angle : 0.730 8.249 6809 Z= 0.378 Chirality : 0.046 0.194 710 Planarity : 0.005 0.055 881 Dihedral : 5.442 29.501 642 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.36 % Allowed : 28.46 % Favored : 67.17 % 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: 0.03 (0.34), residues: 595 helix: 0.54 (0.24), residues: 391 sheet: -3.62 (1.26), residues: 10 loop : -0.65 (0.49), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 496 TYR 0.022 0.002 TYR A 367 PHE 0.022 0.002 PHE A 351 TRP 0.014 0.002 TRP A 548 HIS 0.006 0.002 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 5007) covalent geometry : angle 0.73028 ( 6803) SS BOND : bond 0.00391 ( 3) SS BOND : angle 0.59458 ( 6) hydrogen bonds : bond 0.06495 ( 297) hydrogen bonds : angle 5.20401 ( 864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.183 Fit side-chains REVERT: A 96 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7028 (mmmt) REVERT: A 153 GLU cc_start: 0.7729 (mp0) cc_final: 0.7440 (mp0) REVERT: A 287 GLN cc_start: 0.6331 (OUTLIER) cc_final: 0.5641 (tt0) REVERT: A 323 LYS cc_start: 0.8037 (mtmm) cc_final: 0.7787 (ptpt) REVERT: A 456 MET cc_start: 0.8115 (mmp) cc_final: 0.7169 (mmt) REVERT: A 592 TRP cc_start: 0.3848 (OUTLIER) cc_final: 0.2591 (m100) outliers start: 23 outliers final: 16 residues processed: 86 average time/residue: 0.0591 time to fit residues: 6.9428 Evaluate side-chains 86 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 592 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 38 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.171248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.146130 restraints weight = 7605.861| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.68 r_work: 0.3786 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5010 Z= 0.146 Angle : 0.656 9.113 6809 Z= 0.334 Chirality : 0.042 0.153 710 Planarity : 0.005 0.054 881 Dihedral : 5.191 29.230 642 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.61 % Allowed : 30.17 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.28 (0.34), residues: 595 helix: 0.76 (0.25), residues: 391 sheet: -3.31 (1.37), residues: 10 loop : -0.65 (0.49), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.015 0.001 TYR A 497 PHE 0.012 0.001 PHE A 351 TRP 0.010 0.001 TRP A 548 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5007) covalent geometry : angle 0.65657 ( 6803) SS BOND : bond 0.00183 ( 3) SS BOND : angle 0.28561 ( 6) hydrogen bonds : bond 0.05531 ( 297) hydrogen bonds : angle 4.95940 ( 864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.186 Fit side-chains REVERT: A 96 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7030 (mmmt) REVERT: A 153 GLU cc_start: 0.7688 (mp0) cc_final: 0.7337 (mp0) REVERT: A 253 TRP cc_start: 0.7950 (OUTLIER) cc_final: 0.7136 (m-90) REVERT: A 256 PHE cc_start: 0.7127 (m-10) cc_final: 0.6272 (m-80) REVERT: A 323 LYS cc_start: 0.8103 (mtmm) cc_final: 0.7859 (ptpt) REVERT: A 477 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7259 (mm-30) REVERT: A 592 TRP cc_start: 0.3812 (OUTLIER) cc_final: 0.2657 (m100) outliers start: 19 outliers final: 13 residues processed: 86 average time/residue: 0.0575 time to fit residues: 6.7985 Evaluate side-chains 84 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 592 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 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 = 0.4231 r_free = 0.4231 target = 0.172090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.147314 restraints weight = 7460.224| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.63 r_work: 0.3807 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5010 Z= 0.145 Angle : 0.664 9.708 6809 Z= 0.333 Chirality : 0.042 0.150 710 Planarity : 0.005 0.055 881 Dihedral : 5.086 29.715 642 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.23 % Allowed : 30.36 % Favored : 66.41 % 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: 0.37 (0.34), residues: 595 helix: 0.83 (0.25), residues: 391 sheet: -3.26 (1.39), residues: 10 loop : -0.59 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 159 TYR 0.017 0.002 TYR A 23 PHE 0.012 0.001 PHE A 351 TRP 0.011 0.001 TRP A 548 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5007) covalent geometry : angle 0.66449 ( 6803) SS BOND : bond 0.00209 ( 3) SS BOND : angle 0.39956 ( 6) hydrogen bonds : bond 0.05451 ( 297) hydrogen bonds : angle 4.90368 ( 864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.113 Fit side-chains REVERT: A 96 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7028 (mmmt) REVERT: A 256 PHE cc_start: 0.7015 (m-10) cc_final: 0.6395 (m-80) REVERT: A 477 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7149 (mm-30) REVERT: A 592 TRP cc_start: 0.3767 (OUTLIER) cc_final: 0.2600 (m100) outliers start: 17 outliers final: 15 residues processed: 81 average time/residue: 0.0450 time to fit residues: 5.1578 Evaluate side-chains 83 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 592 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 15 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.172584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.147304 restraints weight = 7630.364| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.69 r_work: 0.3802 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5010 Z= 0.152 Angle : 0.675 8.527 6809 Z= 0.341 Chirality : 0.042 0.154 710 Planarity : 0.005 0.055 881 Dihedral : 5.122 29.768 642 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.42 % Allowed : 29.98 % Favored : 66.60 % 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: 0.37 (0.34), residues: 595 helix: 0.82 (0.25), residues: 391 sheet: -3.00 (1.35), residues: 10 loop : -0.59 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 500 TYR 0.017 0.002 TYR A 497 PHE 0.015 0.001 PHE A 297 TRP 0.011 0.001 TRP A 548 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 5007) covalent geometry : angle 0.67473 ( 6803) SS BOND : bond 0.00298 ( 3) SS BOND : angle 0.51430 ( 6) hydrogen bonds : bond 0.05527 ( 297) hydrogen bonds : angle 4.89360 ( 864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.183 Fit side-chains REVERT: A 96 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7041 (mmmt) REVERT: A 153 GLU cc_start: 0.7627 (mp0) cc_final: 0.7273 (mp0) REVERT: A 253 TRP cc_start: 0.7895 (OUTLIER) cc_final: 0.7214 (m-90) REVERT: A 256 PHE cc_start: 0.7045 (m-10) cc_final: 0.6406 (m-80) REVERT: A 592 TRP cc_start: 0.3849 (OUTLIER) cc_final: 0.2685 (m100) outliers start: 18 outliers final: 14 residues processed: 81 average time/residue: 0.0420 time to fit residues: 4.9504 Evaluate side-chains 83 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 592 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 0.0770 chunk 20 optimal weight: 0.9980 overall best weight: 0.5540 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.174564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.149729 restraints weight = 7549.878| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.66 r_work: 0.3832 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5010 Z= 0.139 Angle : 0.666 8.524 6809 Z= 0.333 Chirality : 0.042 0.151 710 Planarity : 0.005 0.055 881 Dihedral : 5.020 29.588 642 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.98 % Allowed : 29.41 % Favored : 66.60 % 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: 0.44 (0.35), residues: 595 helix: 0.89 (0.25), residues: 393 sheet: -2.89 (1.34), residues: 10 loop : -0.61 (0.51), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 500 TYR 0.017 0.001 TYR A 23 PHE 0.010 0.001 PHE A 351 TRP 0.009 0.001 TRP A 548 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5007) covalent geometry : angle 0.66649 ( 6803) SS BOND : bond 0.00243 ( 3) SS BOND : angle 0.45179 ( 6) hydrogen bonds : bond 0.05273 ( 297) hydrogen bonds : angle 4.85374 ( 864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1020.49 seconds wall clock time: 18 minutes 9.10 seconds (1089.10 seconds total)