Starting phenix.real_space_refine on Wed Sep 17 06:12:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kmm_62438/09_2025/9kmm_62438.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kmm_62438/09_2025/9kmm_62438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kmm_62438/09_2025/9kmm_62438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kmm_62438/09_2025/9kmm_62438.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kmm_62438/09_2025/9kmm_62438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kmm_62438/09_2025/9kmm_62438.map" } resolution = 3.3 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= 0.025 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: 6 Type Number sf(0) Gaussians S 41 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3892 2.51 5 N 940 2.21 5 O 1055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5931 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 922 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "A" Number of atoms: 4193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4193 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 804 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Unusual residues: {' CL': 1, ' NA': 2, 'IZC': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.75, per 1000 atoms: 0.30 Number of scatterers: 5931 At special positions: 0 Unit cell: (72.98, 82.82, 112.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 41 16.00 Na 2 11.00 O 1055 8.00 N 940 7.00 C 3892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " 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: 0.63 Conformation dependent library (CDL) restraints added in 229.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1364 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 50.7% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.601A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.681A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.978A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 90 through 105 Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 122 through 151 Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 219 through 233 Processing helix chain 'A' and resid 251 through 265 Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.820A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.764A pdb=" N SER A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 356 Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 383 through 418 Processing helix chain 'A' and resid 425 through 442 removed outlier: 3.757A pdb=" N ILE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.922A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 496 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.576A pdb=" N LEU A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.014A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.235A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.551A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLY H 16 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER H 85 " --> pdb=" O GLY H 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.583A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR H 94 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.583A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR H 94 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6 removed outlier: 12.089A pdb=" N CYS L 23 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N THR L 75 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N ALA L 25 " --> pdb=" O SER L 73 " (cutoff:3.500A) removed outlier: 11.094A pdb=" N SER L 73 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.986A pdb=" N SER L 27 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER L 71 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY L 69 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.344A pdb=" N MET L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 885 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: 0.99 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1712 1.34 - 1.46: 1446 1.46 - 1.58: 2881 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 6099 Sorted by residual: bond pdb=" C4 IZC A1002 " pdb=" C5 IZC A1002 " ideal model delta sigma weight residual 1.482 1.355 0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C2 IZC A1002 " pdb=" N1 IZC A1002 " ideal model delta sigma weight residual 1.441 1.336 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C2 IZC A1002 " pdb=" N3 IZC A1002 " ideal model delta sigma weight residual 1.437 1.337 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C PHE A 67 " pdb=" N PRO A 68 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.09e+00 bond pdb=" CG LEU A 398 " pdb=" CD1 LEU A 398 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.88e+00 ... (remaining 6094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 8111 2.77 - 5.54: 154 5.54 - 8.31: 21 8.31 - 11.07: 3 11.07 - 13.84: 2 Bond angle restraints: 8291 Sorted by residual: angle pdb=" C SER L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.54 131.46 -9.92 1.91e+00 2.74e-01 2.70e+01 angle pdb=" C4 IZC A1002 " pdb=" C6 IZC A1002 " pdb=" C7 IZC A1002 " ideal model delta sigma weight residual 121.54 107.70 13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" C TRP A 218 " pdb=" N ASP A 219 " pdb=" CA ASP A 219 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" CB MET A 452 " pdb=" CG MET A 452 " pdb=" SD MET A 452 " ideal model delta sigma weight residual 112.70 124.48 -11.78 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C GLY L 30 " pdb=" N SER L 31 " pdb=" CA SER L 31 " ideal model delta sigma weight residual 121.54 128.56 -7.02 1.91e+00 2.74e-01 1.35e+01 ... (remaining 8286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 3102 16.36 - 32.71: 308 32.71 - 49.07: 69 49.07 - 65.42: 11 65.42 - 81.78: 6 Dihedral angle restraints: 3496 sinusoidal: 1337 harmonic: 2159 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual 93.00 174.78 -81.78 1 1.00e+01 1.00e-02 8.23e+01 dihedral pdb=" CA TYR L 95 " pdb=" C TYR L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA SER L 31 " pdb=" C SER L 31 " pdb=" N SER L 32 " pdb=" CA SER L 32 " ideal model delta harmonic sigma weight residual 180.00 157.50 22.50 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 3493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 707 0.057 - 0.113: 157 0.113 - 0.170: 36 0.170 - 0.226: 6 0.226 - 0.283: 2 Chirality restraints: 908 Sorted by residual: chirality pdb=" CB VAL A 140 " pdb=" CA VAL A 140 " pdb=" CG1 VAL A 140 " pdb=" CG2 VAL A 140 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE H 70 " pdb=" CA ILE H 70 " pdb=" CG1 ILE H 70 " pdb=" CG2 ILE H 70 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU A 312 " pdb=" CB LEU A 312 " pdb=" CD1 LEU A 312 " pdb=" CD2 LEU A 312 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 905 not shown) Planarity restraints: 1022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 92 " -0.051 5.00e-02 4.00e+02 7.63e-02 9.31e+00 pdb=" N PRO A 93 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 479 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" C ILE A 479 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE A 479 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA A 480 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 219 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.80e+00 pdb=" C ASP A 219 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP A 219 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 220 " -0.016 2.00e-02 2.50e+03 ... (remaining 1019 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 858 2.76 - 3.29: 5637 3.29 - 3.83: 10607 3.83 - 4.36: 12692 4.36 - 4.90: 21815 Nonbonded interactions: 51609 Sorted by model distance: nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 103 " model vdw 2.221 3.040 nonbonded pdb=" O ASP A 459 " pdb=" OG SER A 464 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.257 3.040 nonbonded pdb=" O ILE A 496 " pdb=" OH TYR L 33 " model vdw 2.276 3.040 ... (remaining 51604 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.910 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.410 ------------------------------------------------------------------------------- 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 : 0.006 0.127 6102 Z= 0.282 Angle : 0.933 13.843 8297 Z= 0.494 Chirality : 0.054 0.283 908 Planarity : 0.008 0.076 1022 Dihedral : 13.928 80.655 2123 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -2.31 (0.28), residues: 745 helix: -1.11 (0.24), residues: 346 sheet: -1.63 (0.52), residues: 106 loop : -1.83 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 499 TYR 0.029 0.002 TYR A 137 PHE 0.031 0.003 PHE A 338 TRP 0.017 0.002 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00634 ( 6099) covalent geometry : angle 0.93227 ( 8291) SS BOND : bond 0.00141 ( 3) SS BOND : angle 1.68508 ( 6) hydrogen bonds : bond 0.16884 ( 305) hydrogen bonds : angle 7.90694 ( 885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 289 GLN cc_start: 0.7850 (pt0) cc_final: 0.7544 (pt0) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0854 time to fit residues: 7.1217 Evaluate side-chains 56 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.242893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.220761 restraints weight = 6128.913| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 1.46 r_work: 0.4162 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6102 Z= 0.186 Angle : 0.617 7.163 8297 Z= 0.325 Chirality : 0.042 0.160 908 Planarity : 0.006 0.069 1022 Dihedral : 5.650 65.051 833 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.47 % Allowed : 7.06 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.30), residues: 745 helix: -0.10 (0.26), residues: 353 sheet: -1.70 (0.52), residues: 101 loop : -1.52 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.021 0.001 TYR A 137 PHE 0.014 0.002 PHE A 338 TRP 0.019 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 6099) covalent geometry : angle 0.61696 ( 8291) SS BOND : bond 0.00163 ( 3) SS BOND : angle 0.72657 ( 6) hydrogen bonds : bond 0.04786 ( 305) hydrogen bonds : angle 5.80405 ( 885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.207 Fit side-chains REVERT: A 401 ASP cc_start: 0.7836 (m-30) cc_final: 0.7560 (m-30) outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 0.0756 time to fit residues: 6.0048 Evaluate side-chains 54 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 25 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.240119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.219197 restraints weight = 6054.814| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 1.35 r_work: 0.4213 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.4066 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6102 Z= 0.196 Angle : 0.603 8.599 8297 Z= 0.315 Chirality : 0.042 0.152 908 Planarity : 0.006 0.065 1022 Dihedral : 5.336 58.195 833 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.26 % Allowed : 9.26 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.30), residues: 745 helix: 0.24 (0.27), residues: 356 sheet: -1.68 (0.53), residues: 98 loop : -1.42 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.021 0.001 TYR A 137 PHE 0.015 0.002 PHE A 392 TRP 0.018 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 6099) covalent geometry : angle 0.60282 ( 8291) SS BOND : bond 0.00147 ( 3) SS BOND : angle 0.66357 ( 6) hydrogen bonds : bond 0.04680 ( 305) hydrogen bonds : angle 5.61479 ( 885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.218 Fit side-chains REVERT: H 93 MET cc_start: 0.7923 (ttm) cc_final: 0.7664 (ttm) REVERT: A 304 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.6953 (tp) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.0991 time to fit residues: 7.9950 Evaluate side-chains 60 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.0270 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.9242 ------------------------------------------------------------------------------- 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 = 0.4570 r_free = 0.4570 target = 0.234822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.211160 restraints weight = 6095.469| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 1.53 r_work: 0.4011 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 6102 Z= 0.255 Angle : 0.657 12.241 8297 Z= 0.339 Chirality : 0.044 0.161 908 Planarity : 0.006 0.065 1022 Dihedral : 5.272 48.691 833 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.98 % Favored : 92.89 % Rotamer: Outliers : 1.57 % Allowed : 11.30 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.31), residues: 745 helix: 0.11 (0.27), residues: 359 sheet: -2.05 (0.50), residues: 103 loop : -1.27 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 499 TYR 0.022 0.002 TYR A 137 PHE 0.018 0.002 PHE A 392 TRP 0.019 0.002 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00608 ( 6099) covalent geometry : angle 0.65750 ( 8291) SS BOND : bond 0.00197 ( 3) SS BOND : angle 0.60685 ( 6) hydrogen bonds : bond 0.04949 ( 305) hydrogen bonds : angle 5.72323 ( 885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.292 Fit side-chains REVERT: A 304 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7129 (tp) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.0986 time to fit residues: 8.5296 Evaluate side-chains 65 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 33 optimal weight: 0.0470 chunk 63 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.4605 r_free = 0.4605 target = 0.239020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.215741 restraints weight = 6189.018| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 1.54 r_work: 0.4144 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6102 Z= 0.173 Angle : 0.586 11.274 8297 Z= 0.303 Chirality : 0.041 0.156 908 Planarity : 0.005 0.060 1022 Dihedral : 4.900 34.217 833 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.58 % Favored : 93.29 % Rotamer: Outliers : 1.41 % Allowed : 12.56 % Favored : 86.03 % 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: -0.98 (0.31), residues: 745 helix: 0.35 (0.27), residues: 362 sheet: -1.85 (0.52), residues: 98 loop : -1.39 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.022 0.001 TYR A 137 PHE 0.016 0.002 PHE A 392 TRP 0.019 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 6099) covalent geometry : angle 0.58637 ( 8291) SS BOND : bond 0.00163 ( 3) SS BOND : angle 0.54903 ( 6) hydrogen bonds : bond 0.04380 ( 305) hydrogen bonds : angle 5.47549 ( 885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.210 Fit side-chains REVERT: A 304 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.6842 (tp) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.1008 time to fit residues: 8.2451 Evaluate side-chains 66 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 14 optimal weight: 0.0870 chunk 50 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.244704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.222943 restraints weight = 6112.990| |-----------------------------------------------------------------------------| r_work (start): 0.4457 rms_B_bonded: 1.46 r_work: 0.4214 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6102 Z= 0.132 Angle : 0.559 14.588 8297 Z= 0.285 Chirality : 0.040 0.205 908 Planarity : 0.005 0.055 1022 Dihedral : 4.664 28.412 833 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 1.73 % Allowed : 13.66 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.72 (0.31), residues: 745 helix: 0.68 (0.27), residues: 359 sheet: -1.98 (0.49), residues: 104 loop : -1.30 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.024 0.001 TYR A 137 PHE 0.013 0.001 PHE A 392 TRP 0.018 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6099) covalent geometry : angle 0.55944 ( 8291) SS BOND : bond 0.00174 ( 3) SS BOND : angle 0.55350 ( 6) hydrogen bonds : bond 0.03997 ( 305) hydrogen bonds : angle 5.18542 ( 885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.229 Fit side-chains REVERT: H 50 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: A 304 ILE cc_start: 0.7188 (OUTLIER) cc_final: 0.6656 (tp) REVERT: L 92 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7003 (m-80) outliers start: 11 outliers final: 5 residues processed: 68 average time/residue: 0.0948 time to fit residues: 8.4346 Evaluate side-chains 64 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 1 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4638 r_free = 0.4638 target = 0.242399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.220327 restraints weight = 6134.957| |-----------------------------------------------------------------------------| r_work (start): 0.4447 rms_B_bonded: 1.46 r_work: 0.4104 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6102 Z= 0.154 Angle : 0.579 13.623 8297 Z= 0.296 Chirality : 0.040 0.181 908 Planarity : 0.005 0.057 1022 Dihedral : 4.673 26.971 833 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.31 % Favored : 93.56 % Rotamer: Outliers : 1.57 % Allowed : 14.76 % Favored : 83.67 % 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: -0.71 (0.31), residues: 745 helix: 0.68 (0.27), residues: 359 sheet: -2.06 (0.49), residues: 106 loop : -1.22 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.022 0.001 TYR A 137 PHE 0.015 0.001 PHE A 392 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6099) covalent geometry : angle 0.57865 ( 8291) SS BOND : bond 0.00147 ( 3) SS BOND : angle 0.50516 ( 6) hydrogen bonds : bond 0.04125 ( 305) hydrogen bonds : angle 5.18895 ( 885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.210 Fit side-chains REVERT: H 50 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: A 304 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.6885 (tp) outliers start: 10 outliers final: 8 residues processed: 59 average time/residue: 0.1026 time to fit residues: 7.8711 Evaluate side-chains 61 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 48 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 7 optimal weight: 0.1980 chunk 57 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4634 r_free = 0.4634 target = 0.241835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.221506 restraints weight = 6096.934| |-----------------------------------------------------------------------------| r_work (start): 0.4454 rms_B_bonded: 1.31 r_work: 0.4199 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6102 Z= 0.157 Angle : 0.589 13.237 8297 Z= 0.300 Chirality : 0.040 0.172 908 Planarity : 0.005 0.058 1022 Dihedral : 4.679 27.034 833 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.04 % Allowed : 14.91 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.72 (0.31), residues: 745 helix: 0.68 (0.27), residues: 359 sheet: -2.09 (0.48), residues: 106 loop : -1.22 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.022 0.001 TYR A 137 PHE 0.015 0.001 PHE A 392 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 6099) covalent geometry : angle 0.58874 ( 8291) SS BOND : bond 0.00148 ( 3) SS BOND : angle 0.48171 ( 6) hydrogen bonds : bond 0.04160 ( 305) hydrogen bonds : angle 5.21070 ( 885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.227 Fit side-chains REVERT: A 304 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6735 (tp) REVERT: L 92 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7031 (m-80) outliers start: 13 outliers final: 10 residues processed: 63 average time/residue: 0.0996 time to fit residues: 8.2506 Evaluate side-chains 63 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 64 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 43 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.237364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.213982 restraints weight = 6187.433| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 1.54 r_work: 0.4116 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6102 Z= 0.202 Angle : 0.620 12.972 8297 Z= 0.317 Chirality : 0.042 0.180 908 Planarity : 0.005 0.059 1022 Dihedral : 4.784 26.761 833 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.04 % Allowed : 15.86 % Favored : 82.10 % 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: -0.80 (0.31), residues: 745 helix: 0.52 (0.27), residues: 356 sheet: -1.94 (0.50), residues: 98 loop : -1.23 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 499 TYR 0.021 0.002 TYR A 137 PHE 0.016 0.002 PHE A 392 TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 6099) covalent geometry : angle 0.62050 ( 8291) SS BOND : bond 0.00163 ( 3) SS BOND : angle 0.51771 ( 6) hydrogen bonds : bond 0.04491 ( 305) hydrogen bonds : angle 5.36102 ( 885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.213 Fit side-chains REVERT: A 304 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.6913 (tp) outliers start: 13 outliers final: 10 residues processed: 63 average time/residue: 0.1016 time to fit residues: 8.2809 Evaluate side-chains 64 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 29 optimal weight: 0.0060 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.4603 r_free = 0.4603 target = 0.238981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.215748 restraints weight = 6155.595| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 1.54 r_work: 0.4065 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6102 Z= 0.174 Angle : 0.605 12.913 8297 Z= 0.307 Chirality : 0.041 0.170 908 Planarity : 0.005 0.059 1022 Dihedral : 4.738 27.385 833 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.73 % Allowed : 16.48 % Favored : 81.79 % 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: -0.77 (0.31), residues: 745 helix: 0.55 (0.27), residues: 356 sheet: -1.93 (0.50), residues: 98 loop : -1.22 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.022 0.001 TYR A 137 PHE 0.015 0.001 PHE A 392 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 6099) covalent geometry : angle 0.60539 ( 8291) SS BOND : bond 0.00140 ( 3) SS BOND : angle 0.49996 ( 6) hydrogen bonds : bond 0.04317 ( 305) hydrogen bonds : angle 5.31189 ( 885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.232 Fit side-chains REVERT: A 304 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.6948 (tp) REVERT: L 92 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7071 (m-80) outliers start: 11 outliers final: 9 residues processed: 61 average time/residue: 0.1036 time to fit residues: 8.2199 Evaluate side-chains 63 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 39 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4619 r_free = 0.4619 target = 0.240713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.218214 restraints weight = 6136.909| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 1.50 r_work: 0.4104 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6102 Z= 0.156 Angle : 0.586 12.878 8297 Z= 0.298 Chirality : 0.040 0.161 908 Planarity : 0.005 0.058 1022 Dihedral : 4.681 27.433 833 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.88 % Allowed : 16.80 % Favored : 81.32 % 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: -0.71 (0.31), residues: 745 helix: 0.62 (0.27), residues: 358 sheet: -1.86 (0.51), residues: 98 loop : -1.25 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.022 0.001 TYR A 137 PHE 0.015 0.001 PHE A 392 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6099) covalent geometry : angle 0.58570 ( 8291) SS BOND : bond 0.00140 ( 3) SS BOND : angle 0.52151 ( 6) hydrogen bonds : bond 0.04188 ( 305) hydrogen bonds : angle 5.22615 ( 885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1561.09 seconds wall clock time: 27 minutes 41.05 seconds (1661.05 seconds total)