Starting phenix.real_space_refine on Wed Mar 5 23:09:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fij_31599/03_2025/7fij_31599.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fij_31599/03_2025/7fij_31599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fij_31599/03_2025/7fij_31599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fij_31599/03_2025/7fij_31599.map" model { file = "/net/cci-nas-00/data/ceres_data/7fij_31599/03_2025/7fij_31599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fij_31599/03_2025/7fij_31599.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1212 atoms to isotropic. 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 4 5.16 5 C 1865 2.51 5 N 594 2.21 5 O 598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3061 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 3061 Classifications: {'peptide': 561} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 412} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 534} Chain breaks: 1 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1442 Unresolved non-hydrogen angles: 1848 Unresolved non-hydrogen dihedrals: 1194 Unresolved non-hydrogen chiralities: 167 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 34, 'GLU:plan': 23, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 673 Time building chain proxies: 2.77, per 1000 atoms: 0.90 Number of scatterers: 3061 At special positions: 0 Unit cell: (61.655, 81.51, 124.355, 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 4 16.00 O 598 8.00 N 594 7.00 C 1865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 439 " - pdb=" SG CYS R 514 " 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: 0.83 Conformation dependent library (CDL) restraints added in 581.8 milliseconds 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1068 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 4 sheets defined 43.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'R' and resid 241 through 245 removed outlier: 4.068A pdb=" N SER R 244 " --> pdb=" O GLY R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 283 Processing helix chain 'R' and resid 362 through 387 removed outlier: 3.961A pdb=" N ILE R 366 " --> pdb=" O LEU R 362 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TRP R 367 " --> pdb=" O ARG R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 420 Processing helix chain 'R' and resid 429 through 435 removed outlier: 3.531A pdb=" N THR R 435 " --> pdb=" O ILE R 431 " (cutoff:3.500A) Processing helix chain 'R' and resid 437 through 468 removed outlier: 3.717A pdb=" N ARG R 464 " --> pdb=" O ILE R 460 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP R 465 " --> pdb=" O THR R 461 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS R 466 " --> pdb=" O LEU R 462 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE R 468 " --> pdb=" O ARG R 464 " (cutoff:3.500A) Processing helix chain 'R' and resid 470 through 477 removed outlier: 5.409A pdb=" N ASP R 475 " --> pdb=" O ILE R 472 " (cutoff:3.500A) Processing helix chain 'R' and resid 479 through 504 Proline residue: R 501 - end of helix removed outlier: 3.772A pdb=" N GLY R 504 " --> pdb=" O LEU R 500 " (cutoff:3.500A) Processing helix chain 'R' and resid 521 through 552 Processing helix chain 'R' and resid 560 through 595 removed outlier: 3.555A pdb=" N CYS R 581 " --> pdb=" O THR R 577 " (cutoff:3.500A) Proline residue: R 584 - end of helix Processing helix chain 'R' and resid 603 through 610 removed outlier: 3.679A pdb=" N LEU R 607 " --> pdb=" O ASN R 603 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU R 608 " --> pdb=" O SER R 604 " (cutoff:3.500A) Processing helix chain 'R' and resid 613 through 624 removed outlier: 4.118A pdb=" N CYS R 617 " --> pdb=" O PRO R 613 " (cutoff:3.500A) Proline residue: R 620 - end of helix Processing helix chain 'R' and resid 627 through 641 Processing sheet with id=AA1, first strand: chain 'R' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'R' and resid 102 through 105 removed outlier: 6.336A pdb=" N ILE R 103 " --> pdb=" O SER R 129 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N CYS R 131 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE R 105 " --> pdb=" O CYS R 131 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL R 177 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER R 201 " --> pdb=" O VAL R 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 163 through 164 removed outlier: 4.163A pdb=" N ILE R 164 " --> pdb=" O GLU R 188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'R' and resid 226 through 228 185 hydrogen bonds defined for protein. 537 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: 0.98 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: 1173 1.34 - 1.46: 569 1.46 - 1.58: 1335 1.58 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3083 Sorted by residual: bond pdb=" CB PRO R 345 " pdb=" CG PRO R 345 " ideal model delta sigma weight residual 1.506 1.484 0.022 3.90e-02 6.57e+02 3.09e-01 bond pdb=" C SER R 512 " pdb=" N ILE R 513 " ideal model delta sigma weight residual 1.338 1.332 0.006 1.01e-02 9.80e+03 3.08e-01 bond pdb=" C VAL R 393 " pdb=" N PRO R 394 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.36e-02 5.41e+03 2.57e-01 bond pdb=" CA TYR R 612 " pdb=" C TYR R 612 " ideal model delta sigma weight residual 1.520 1.526 -0.006 1.23e-02 6.61e+03 2.44e-01 bond pdb=" CA TYR R 275 " pdb=" CB TYR R 275 " ideal model delta sigma weight residual 1.522 1.530 -0.008 1.71e-02 3.42e+03 2.24e-01 ... (remaining 3078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 4246 1.64 - 3.28: 23 3.28 - 4.91: 8 4.91 - 6.55: 1 6.55 - 8.19: 1 Bond angle restraints: 4279 Sorted by residual: angle pdb=" N ILE R 513 " pdb=" CA ILE R 513 " pdb=" C ILE R 513 " ideal model delta sigma weight residual 112.98 109.68 3.30 1.25e+00 6.40e-01 6.95e+00 angle pdb=" CA LEU R 122 " pdb=" CB LEU R 122 " pdb=" CG LEU R 122 " ideal model delta sigma weight residual 116.30 124.49 -8.19 3.50e+00 8.16e-02 5.47e+00 angle pdb=" N ASN R 132 " pdb=" CA ASN R 132 " pdb=" CB ASN R 132 " ideal model delta sigma weight residual 113.65 110.34 3.31 1.47e+00 4.63e-01 5.06e+00 angle pdb=" C SER R 253 " pdb=" N TYR R 254 " pdb=" CA TYR R 254 " ideal model delta sigma weight residual 121.54 125.21 -3.67 1.91e+00 2.74e-01 3.70e+00 angle pdb=" N ILE R 625 " pdb=" CA ILE R 625 " pdb=" C ILE R 625 " ideal model delta sigma weight residual 109.34 112.81 -3.47 2.08e+00 2.31e-01 2.78e+00 ... (remaining 4274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.22: 1752 14.22 - 28.44: 40 28.44 - 42.66: 12 42.66 - 56.88: 0 56.88 - 71.10: 3 Dihedral angle restraints: 1807 sinusoidal: 175 harmonic: 1632 Sorted by residual: dihedral pdb=" CB CYS R 439 " pdb=" SG CYS R 439 " pdb=" SG CYS R 514 " pdb=" CB CYS R 514 " ideal model delta sinusoidal sigma weight residual 93.00 31.48 61.52 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" N ASN R 207 " pdb=" CA ASN R 207 " pdb=" CB ASN R 207 " pdb=" CG ASN R 207 " ideal model delta sinusoidal sigma weight residual -180.00 -141.07 -38.93 3 1.50e+01 4.44e-03 6.88e+00 dihedral pdb=" CA ALA R 560 " pdb=" C ALA R 560 " pdb=" N THR R 561 " pdb=" CA THR R 561 " ideal model delta harmonic sigma weight residual -180.00 -167.09 -12.91 0 5.00e+00 4.00e-02 6.67e+00 ... (remaining 1804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 307 0.026 - 0.053: 146 0.053 - 0.079: 67 0.079 - 0.106: 30 0.106 - 0.132: 12 Chirality restraints: 562 Sorted by residual: chirality pdb=" CA ILE R 64 " pdb=" N ILE R 64 " pdb=" C ILE R 64 " pdb=" CB ILE R 64 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE R 78 " pdb=" N ILE R 78 " pdb=" C ILE R 78 " pdb=" CB ILE R 78 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA ILE R 155 " pdb=" N ILE R 155 " pdb=" C ILE R 155 " pdb=" CB ILE R 155 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 559 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR R 612 " -0.012 5.00e-02 4.00e+02 1.87e-02 5.62e-01 pdb=" N PRO R 613 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO R 613 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO R 613 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 561 " 0.003 2.00e-02 2.50e+03 5.22e-03 2.72e-01 pdb=" C THR R 561 " -0.009 2.00e-02 2.50e+03 pdb=" O THR R 561 " 0.003 2.00e-02 2.50e+03 pdb=" N ASN R 562 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 579 " 0.002 2.00e-02 2.50e+03 4.55e-03 2.07e-01 pdb=" C PHE R 579 " -0.008 2.00e-02 2.50e+03 pdb=" O PHE R 579 " 0.003 2.00e-02 2.50e+03 pdb=" N THR R 580 " 0.003 2.00e-02 2.50e+03 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 1194 2.86 - 3.37: 2958 3.37 - 3.88: 4765 3.88 - 4.39: 4448 4.39 - 4.90: 8351 Nonbonded interactions: 21716 Sorted by model distance: nonbonded pdb=" O THR R 133 " pdb=" ND2 ASN R 158 " model vdw 2.344 3.120 nonbonded pdb=" O ILE R 76 " pdb=" N SER R 101 " model vdw 2.398 3.120 nonbonded pdb=" O LEU R 638 " pdb=" N CYS R 644 " model vdw 2.402 3.120 nonbonded pdb=" O ASP R 419 " pdb=" OG1 THR R 422 " model vdw 2.406 3.040 nonbonded pdb=" N ILE R 229 " pdb=" O ILE R 249 " model vdw 2.411 3.120 ... (remaining 21711 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.500 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5027 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 : 0.001 0.022 3083 Z= 0.094 Angle : 0.412 8.189 4279 Z= 0.237 Chirality : 0.042 0.132 562 Planarity : 0.001 0.019 603 Dihedral : 8.017 71.101 736 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.39), residues: 557 helix: 3.63 (0.34), residues: 214 sheet: -1.28 (0.74), residues: 49 loop : -1.24 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP R 367 HIS 0.001 0.000 HIS R 278 PHE 0.003 0.000 PHE R 265 TYR 0.006 0.001 TYR R 427 ARG 0.001 0.000 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.325 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0721 time to fit residues: 3.9234 Evaluate side-chains 35 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 43 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.4617 r_free = 0.4617 target = 0.216278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.209747 restraints weight = 6258.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.209345 restraints weight = 8487.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.209901 restraints weight = 6593.077| |-----------------------------------------------------------------------------| r_work (final): 0.4540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4540 r_free = 0.4540 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4540 r_free = 0.4540 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5239 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3083 Z= 0.228 Angle : 0.512 7.588 4279 Z= 0.298 Chirality : 0.045 0.187 562 Planarity : 0.003 0.035 603 Dihedral : 4.263 18.769 567 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.00 % Allowed : 7.50 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.38), residues: 557 helix: 3.18 (0.35), residues: 210 sheet: -1.39 (0.77), residues: 47 loop : -1.46 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 367 HIS 0.003 0.002 HIS R 214 PHE 0.014 0.001 PHE R 265 TYR 0.009 0.001 TYR R 359 ARG 0.012 0.003 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.337 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.0715 time to fit residues: 4.3980 Evaluate side-chains 39 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 5 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 207 ASN ** 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 = 0.4496 r_free = 0.4496 target = 0.205265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.200895 restraints weight = 5887.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.200641 restraints weight = 7730.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.200739 restraints weight = 7332.495| |-----------------------------------------------------------------------------| r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4444 r_free = 0.4444 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4444 r_free = 0.4444 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5546 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 3083 Z= 0.576 Angle : 0.884 11.471 4279 Z= 0.526 Chirality : 0.054 0.200 562 Planarity : 0.006 0.043 603 Dihedral : 7.890 28.612 567 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 8.75 % Allowed : 21.25 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.35), residues: 557 helix: 1.23 (0.34), residues: 208 sheet: -2.36 (0.75), residues: 48 loop : -2.68 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 367 HIS 0.019 0.006 HIS R 214 PHE 0.045 0.003 PHE R 265 TYR 0.021 0.003 TYR R 240 ARG 0.027 0.005 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.300 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.0633 time to fit residues: 4.0976 Evaluate side-chains 40 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 429 HIS Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 34 optimal weight: 0.0470 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 207 ASN ** 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 = 0.4551 r_free = 0.4551 target = 0.209998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.205062 restraints weight = 6181.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.204699 restraints weight = 10155.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.204912 restraints weight = 8338.048| |-----------------------------------------------------------------------------| r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4476 r_free = 0.4476 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4476 r_free = 0.4476 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5411 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3083 Z= 0.220 Angle : 0.559 8.231 4279 Z= 0.327 Chirality : 0.045 0.145 562 Planarity : 0.003 0.033 603 Dihedral : 5.914 20.302 567 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 3.75 % Allowed : 25.00 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.37), residues: 557 helix: 2.22 (0.36), residues: 204 sheet: -2.16 (0.80), residues: 47 loop : -2.44 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 491 HIS 0.006 0.002 HIS R 214 PHE 0.014 0.001 PHE R 265 TYR 0.010 0.001 TYR R 427 ARG 0.009 0.002 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.390 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.0685 time to fit residues: 4.2087 Evaluate side-chains 39 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 429 HIS Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 5 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 207 ASN ** 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 = 0.4533 r_free = 0.4533 target = 0.208612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.204064 restraints weight = 6091.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.203289 restraints weight = 10230.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.203610 restraints weight = 9317.141| |-----------------------------------------------------------------------------| r_work (final): 0.4475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4475 r_free = 0.4475 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4475 r_free = 0.4475 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5452 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3083 Z= 0.288 Angle : 0.617 9.166 4279 Z= 0.359 Chirality : 0.047 0.157 562 Planarity : 0.003 0.033 603 Dihedral : 6.265 20.904 567 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.46 % Favored : 86.54 % Rotamer: Outliers : 8.75 % Allowed : 25.00 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.37), residues: 557 helix: 1.96 (0.35), residues: 214 sheet: -2.32 (0.81), residues: 45 loop : -2.68 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 491 HIS 0.006 0.002 HIS R 214 PHE 0.024 0.001 PHE R 265 TYR 0.012 0.002 TYR R 427 ARG 0.012 0.002 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.261 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.0631 time to fit residues: 4.0043 Evaluate side-chains 42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 429 HIS Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 46 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 0.0770 chunk 49 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 207 ASN ** 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 = 0.4539 r_free = 0.4539 target = 0.209179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.203410 restraints weight = 6224.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.202740 restraints weight = 8643.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.202916 restraints weight = 8954.595| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4451 r_free = 0.4451 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4451 r_free = 0.4451 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5468 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3083 Z= 0.251 Angle : 0.582 8.515 4279 Z= 0.339 Chirality : 0.046 0.148 562 Planarity : 0.003 0.032 603 Dihedral : 6.025 21.155 567 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 7.50 % Allowed : 27.50 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.38), residues: 557 helix: 2.06 (0.35), residues: 214 sheet: -2.68 (0.83), residues: 43 loop : -2.57 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 491 HIS 0.005 0.002 HIS R 214 PHE 0.018 0.001 PHE R 265 TYR 0.012 0.002 TYR R 427 ARG 0.010 0.002 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.343 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 41 average time/residue: 0.0693 time to fit residues: 4.4533 Evaluate side-chains 43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 429 HIS Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.0370 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 207 ASN ** 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 = 0.4532 r_free = 0.4532 target = 0.208681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.204394 restraints weight = 6113.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.204056 restraints weight = 8538.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.204097 restraints weight = 7534.340| |-----------------------------------------------------------------------------| r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4464 r_free = 0.4464 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4464 r_free = 0.4464 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3083 Z= 0.250 Angle : 0.589 8.780 4279 Z= 0.342 Chirality : 0.046 0.149 562 Planarity : 0.003 0.031 603 Dihedral : 5.997 21.360 567 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % Rotamer: Outliers : 8.75 % Allowed : 27.50 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.38), residues: 557 helix: 2.09 (0.35), residues: 214 sheet: -2.76 (0.83), residues: 43 loop : -2.57 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 491 HIS 0.005 0.002 HIS R 214 PHE 0.017 0.001 PHE R 265 TYR 0.011 0.002 TYR R 427 ARG 0.009 0.002 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.312 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 41 average time/residue: 0.0673 time to fit residues: 4.3446 Evaluate side-chains 43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 429 HIS Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 0.0970 chunk 51 optimal weight: 0.4980 chunk 34 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 41 optimal weight: 0.0980 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 0.0470 chunk 37 optimal weight: 2.9990 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.213781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.208224 restraints weight = 6240.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.207770 restraints weight = 8599.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.208011 restraints weight = 7776.130| |-----------------------------------------------------------------------------| r_work (final): 0.4520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4520 r_free = 0.4520 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4520 r_free = 0.4520 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5299 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3083 Z= 0.129 Angle : 0.481 7.289 4279 Z= 0.274 Chirality : 0.044 0.146 562 Planarity : 0.002 0.026 603 Dihedral : 4.528 16.849 567 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 6.25 % Allowed : 30.00 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.40), residues: 557 helix: 2.91 (0.35), residues: 207 sheet: -2.23 (0.93), residues: 38 loop : -2.11 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 491 HIS 0.001 0.000 HIS R 429 PHE 0.004 0.000 PHE R 265 TYR 0.006 0.001 TYR R 427 ARG 0.002 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.326 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 39 average time/residue: 0.0687 time to fit residues: 4.2237 Evaluate side-chains 41 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 429 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 246 GLN R 278 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.205231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.201551 restraints weight = 5999.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.197722 restraints weight = 7593.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.198032 restraints weight = 6723.144| |-----------------------------------------------------------------------------| r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4367 r_free = 0.4367 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4367 r_free = 0.4367 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5647 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 3083 Z= 0.519 Angle : 0.798 11.901 4279 Z= 0.467 Chirality : 0.051 0.174 562 Planarity : 0.005 0.037 603 Dihedral : 7.016 27.799 567 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.08 % Favored : 84.92 % Rotamer: Outliers : 11.25 % Allowed : 26.25 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.37), residues: 557 helix: 1.60 (0.34), residues: 215 sheet: -2.64 (0.83), residues: 41 loop : -2.89 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 367 HIS 0.014 0.005 HIS R 214 PHE 0.037 0.002 PHE R 265 TYR 0.021 0.004 TYR R 240 ARG 0.021 0.005 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.347 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 41 average time/residue: 0.0717 time to fit residues: 4.5987 Evaluate side-chains 44 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 429 HIS Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4527 r_free = 0.4527 target = 0.208454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.204152 restraints weight = 6074.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.203812 restraints weight = 7931.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.202546 restraints weight = 7683.421| |-----------------------------------------------------------------------------| r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4447 r_free = 0.4447 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4447 r_free = 0.4447 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5493 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3083 Z= 0.243 Angle : 0.604 8.371 4279 Z= 0.349 Chirality : 0.047 0.155 562 Planarity : 0.003 0.029 603 Dihedral : 6.074 19.920 567 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 7.50 % Allowed : 31.25 % Favored : 61.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.37), residues: 557 helix: 2.00 (0.35), residues: 214 sheet: -3.05 (1.83), residues: 10 loop : -2.89 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 491 HIS 0.004 0.002 HIS R 429 PHE 0.015 0.001 PHE R 265 TYR 0.010 0.002 TYR R 427 ARG 0.010 0.002 ARG R 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.507 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.0647 time to fit residues: 4.1932 Evaluate side-chains 39 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 429 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4525 r_free = 0.4525 target = 0.208304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.204704 restraints weight = 6069.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.201229 restraints weight = 8279.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.201408 restraints weight = 8022.203| |-----------------------------------------------------------------------------| r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4432 r_free = 0.4432 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4432 r_free = 0.4432 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5520 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3083 Z= 0.254 Angle : 0.606 8.838 4279 Z= 0.348 Chirality : 0.046 0.153 562 Planarity : 0.003 0.030 603 Dihedral : 5.993 23.195 567 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.46 % Favored : 86.54 % Rotamer: Outliers : 7.50 % Allowed : 31.25 % Favored : 61.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.38), residues: 557 helix: 2.06 (0.35), residues: 216 sheet: -2.38 (0.89), residues: 40 loop : -2.91 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 491 HIS 0.005 0.002 HIS R 214 PHE 0.015 0.001 PHE R 265 TYR 0.012 0.002 TYR R 275 ARG 0.009 0.002 ARG R 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1251.00 seconds wall clock time: 22 minutes 18.11 seconds (1338.11 seconds total)