Starting phenix.real_space_refine on Thu Jul 24 09:39:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kmk_62436/07_2025/9kmk_62436.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kmk_62436/07_2025/9kmk_62436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kmk_62436/07_2025/9kmk_62436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kmk_62436/07_2025/9kmk_62436.map" model { file = "/net/cci-nas-00/data/ceres_data/9kmk_62436/07_2025/9kmk_62436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kmk_62436/07_2025/9kmk_62436.cif" } resolution = 3.06 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= -0.000 sd= 0.024 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: 5 Type Number sf(0) Gaussians S 41 5.16 5 Cl 1 4.86 5 C 3854 2.51 5 N 931 2.21 5 O 1045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5872 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: "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: 4145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4145 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 25, 'TRANS': 494} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.17, per 1000 atoms: 0.71 Number of scatterers: 5872 At special positions: 0 Unit cell: (75.44, 82.82, 113.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 41 16.00 O 1045 8.00 N 931 7.00 C 3854 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 L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " 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: 1.36 Conformation dependent library (CDL) restraints added in 794.2 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 6 sheets defined 53.4% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.978A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.940A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.837A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 removed outlier: 4.118A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.243A 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 removed outlier: 3.524A pdb=" N THR A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 4.313A pdb=" N THR A 111 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP A 113 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 151 removed outlier: 4.074A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 236 removed outlier: 3.982A pdb=" N TRP A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 266 removed outlier: 3.710A pdb=" N TYR A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.664A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.571A pdb=" N GLY A 286 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 312 removed outlier: 3.991A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 355 removed outlier: 3.513A pdb=" N CYS A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.574A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 444 removed outlier: 3.692A pdb=" N ILE A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.680A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.778A pdb=" N LEU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 539 through 555 Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 581 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.040A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N CYS H 96 " --> pdb=" O GLY H 110 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR H 94 " --> pdb=" O GLY H 112 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR H 114 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA H 92 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 6 removed outlier: 12.362A pdb=" N CYS L 23 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 11.583A pdb=" N THR L 75 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N ALA L 25 " --> pdb=" O SER L 73 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N SER L 73 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N SER L 27 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER L 71 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY L 69 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.469A pdb=" N MET L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'L' and resid 54 through 55 removed outlier: 5.793A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 531 through 532 318 hydrogen bonds defined for protein. 921 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: 1.61 Time building geometry restraints manager: 1.57 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: 1737 1.34 - 1.46: 1399 1.46 - 1.58: 2845 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6041 Sorted by residual: bond pdb=" CB ILE A 141 " pdb=" CG1 ILE A 141 " ideal model delta sigma weight residual 1.530 1.493 0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" CB VAL A 140 " pdb=" CG1 VAL A 140 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.39e+00 bond pdb=" CG1 ILE A 292 " pdb=" CD1 ILE A 292 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.70e+00 bond pdb=" SD MET A 452 " pdb=" CE MET A 452 " ideal model delta sigma weight residual 1.791 1.750 0.041 2.50e-02 1.60e+03 2.69e+00 bond pdb=" CB VAL A 94 " pdb=" CG2 VAL A 94 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.27e+00 ... (remaining 6036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 7934 2.23 - 4.46: 222 4.46 - 6.69: 43 6.69 - 8.92: 11 8.92 - 11.15: 3 Bond angle restraints: 8213 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 121.54 132.69 -11.15 1.91e+00 2.74e-01 3.41e+01 angle pdb=" C LYS A 317 " pdb=" N TYR A 318 " pdb=" CA TYR A 318 " ideal model delta sigma weight residual 120.79 127.27 -6.48 1.39e+00 5.18e-01 2.17e+01 angle pdb=" N GLY A 62 " pdb=" CA GLY A 62 " pdb=" C GLY A 62 " ideal model delta sigma weight residual 113.18 103.70 9.48 2.37e+00 1.78e-01 1.60e+01 angle pdb=" N TYR A 318 " pdb=" CA TYR A 318 " pdb=" C TYR A 318 " ideal model delta sigma weight residual 111.02 115.88 -4.86 1.22e+00 6.72e-01 1.59e+01 angle pdb=" C ARG A 427 " pdb=" N ARG A 428 " pdb=" CA ARG A 428 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.52e+01 ... (remaining 8208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 3109 17.40 - 34.81: 299 34.81 - 52.21: 44 52.21 - 69.62: 6 69.62 - 87.02: 5 Dihedral angle restraints: 3463 sinusoidal: 1323 harmonic: 2140 Sorted by residual: dihedral pdb=" CA TYR A 320 " pdb=" C TYR A 320 " pdb=" N ASN A 321 " pdb=" CA ASN A 321 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA CYS A 171 " pdb=" C CYS A 171 " pdb=" N MET A 172 " pdb=" CA MET A 172 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+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 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 3460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 828 0.104 - 0.208: 68 0.208 - 0.312: 2 0.312 - 0.417: 0 0.417 - 0.521: 1 Chirality restraints: 899 Sorted by residual: chirality pdb=" CB VAL A 447 " pdb=" CA VAL A 447 " pdb=" CG1 VAL A 447 " pdb=" CG2 VAL A 447 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.78e+00 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 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB THR H 28 " pdb=" CA THR H 28 " pdb=" OG1 THR H 28 " pdb=" CG2 THR H 28 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 896 not shown) Planarity restraints: 1013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 67 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO A 68 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.26e+00 pdb=" N PRO L 8 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 40 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO H 41 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " 0.030 5.00e-02 4.00e+02 ... (remaining 1010 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1413 2.78 - 3.31: 5450 3.31 - 3.84: 10532 3.84 - 4.37: 12363 4.37 - 4.90: 21317 Nonbonded interactions: 51075 Sorted by model distance: nonbonded pdb=" O SER H 52 " pdb=" NH1 ARG H 72 " model vdw 2.256 3.120 nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR A 168 " pdb=" OE2 GLU A 197 " model vdw 2.284 3.040 nonbonded pdb=" OH TYR H 59 " pdb=" OD1 ASP A 494 " model vdw 2.286 3.040 nonbonded pdb=" O SER A 464 " pdb=" OG SER A 464 " model vdw 2.291 3.040 ... (remaining 51070 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.230 Find NCS groups from input model: 0.060 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 0.007 0.072 6044 Z= 0.278 Angle : 0.938 11.151 8219 Z= 0.512 Chirality : 0.058 0.521 899 Planarity : 0.007 0.057 1013 Dihedral : 13.803 87.023 2102 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.99 (0.28), residues: 738 helix: -1.03 (0.23), residues: 367 sheet: -0.64 (0.52), residues: 104 loop : -1.81 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 65 HIS 0.003 0.001 HIS A 151 PHE 0.031 0.003 PHE L 92 TYR 0.022 0.002 TYR A 318 ARG 0.006 0.001 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.16568 ( 318) hydrogen bonds : angle 7.64460 ( 921) SS BOND : bond 0.00148 ( 3) SS BOND : angle 1.70254 ( 6) covalent geometry : bond 0.00669 ( 6041) covalent geometry : angle 0.93681 ( 8213) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.608 Fit side-chains REVERT: A 140 VAL cc_start: 0.8443 (p) cc_final: 0.8127 (m) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1718 time to fit residues: 23.3841 Evaluate side-chains 90 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.0970 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.169828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137266 restraints weight = 6566.282| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.04 r_work: 0.3421 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6044 Z= 0.158 Angle : 0.610 7.994 8219 Z= 0.323 Chirality : 0.043 0.153 899 Planarity : 0.005 0.044 1013 Dihedral : 5.003 24.310 819 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.16 % Allowed : 7.12 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.30), residues: 738 helix: 0.20 (0.25), residues: 375 sheet: -1.00 (0.48), residues: 114 loop : -1.42 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 PHE 0.020 0.002 PHE A 455 TYR 0.019 0.001 TYR A 137 ARG 0.002 0.000 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 318) hydrogen bonds : angle 5.38866 ( 921) SS BOND : bond 0.00127 ( 3) SS BOND : angle 1.55310 ( 6) covalent geometry : bond 0.00354 ( 6041) covalent geometry : angle 0.60839 ( 8213) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.599 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.2171 time to fit residues: 28.5867 Evaluate side-chains 86 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 29 optimal weight: 0.0770 chunk 26 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 0.0370 chunk 41 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 103 GLN A 333 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145912 restraints weight = 6601.882| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.84 r_work: 0.3521 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6044 Z= 0.147 Angle : 0.569 7.389 8219 Z= 0.300 Chirality : 0.041 0.149 899 Planarity : 0.004 0.039 1013 Dihedral : 4.635 21.369 819 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.42 % Allowed : 8.39 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.30), residues: 738 helix: 0.77 (0.26), residues: 376 sheet: -0.88 (0.48), residues: 113 loop : -1.21 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 PHE 0.018 0.001 PHE A 300 TYR 0.020 0.001 TYR A 137 ARG 0.006 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 318) hydrogen bonds : angle 4.96349 ( 921) SS BOND : bond 0.00120 ( 3) SS BOND : angle 1.31323 ( 6) covalent geometry : bond 0.00332 ( 6041) covalent geometry : angle 0.56829 ( 8213) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.644 Fit side-chains REVERT: A 441 LEU cc_start: 0.8554 (mp) cc_final: 0.8283 (mm) REVERT: A 567 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7787 (mtt180) outliers start: 9 outliers final: 5 residues processed: 102 average time/residue: 0.2000 time to fit residues: 26.5181 Evaluate side-chains 93 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 485 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 23 optimal weight: 0.0970 chunk 24 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.176065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.144277 restraints weight = 6710.050| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.91 r_work: 0.3488 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6044 Z= 0.132 Angle : 0.559 8.495 8219 Z= 0.293 Chirality : 0.041 0.162 899 Planarity : 0.004 0.039 1013 Dihedral : 4.471 20.084 819 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.74 % Allowed : 11.08 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.31), residues: 738 helix: 1.11 (0.26), residues: 376 sheet: -0.78 (0.48), residues: 113 loop : -1.15 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 218 HIS 0.002 0.001 HIS A 151 PHE 0.017 0.001 PHE A 300 TYR 0.021 0.001 TYR A 137 ARG 0.005 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 318) hydrogen bonds : angle 4.78474 ( 921) SS BOND : bond 0.00119 ( 3) SS BOND : angle 1.08629 ( 6) covalent geometry : bond 0.00294 ( 6041) covalent geometry : angle 0.55822 ( 8213) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.595 Fit side-chains REVERT: A 441 LEU cc_start: 0.8535 (mp) cc_final: 0.8271 (mm) REVERT: A 567 ARG cc_start: 0.8241 (mtm-85) cc_final: 0.7789 (mtt180) outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 0.2078 time to fit residues: 27.4741 Evaluate side-chains 100 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.0070 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 23 optimal weight: 0.0870 chunk 37 optimal weight: 0.5980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.176402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.144412 restraints weight = 6595.285| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.93 r_work: 0.3504 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6044 Z= 0.136 Angle : 0.570 14.478 8219 Z= 0.294 Chirality : 0.041 0.167 899 Planarity : 0.004 0.038 1013 Dihedral : 4.366 18.745 819 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.06 % Allowed : 11.08 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.31), residues: 738 helix: 1.28 (0.26), residues: 376 sheet: -0.78 (0.47), residues: 113 loop : -1.09 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 218 HIS 0.002 0.000 HIS A 151 PHE 0.017 0.001 PHE A 300 TYR 0.021 0.001 TYR A 137 ARG 0.006 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 318) hydrogen bonds : angle 4.68808 ( 921) SS BOND : bond 0.00128 ( 3) SS BOND : angle 1.27099 ( 6) covalent geometry : bond 0.00308 ( 6041) covalent geometry : angle 0.56957 ( 8213) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.662 Fit side-chains REVERT: L 107 MET cc_start: 0.8241 (mmm) cc_final: 0.7959 (mmt) REVERT: A 212 ASN cc_start: 0.7982 (t0) cc_final: 0.7761 (t0) REVERT: A 441 LEU cc_start: 0.8509 (mp) cc_final: 0.8255 (mm) REVERT: A 498 TYR cc_start: 0.8943 (p90) cc_final: 0.8703 (p90) REVERT: A 567 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.7804 (mtt180) outliers start: 13 outliers final: 11 residues processed: 108 average time/residue: 0.1972 time to fit residues: 27.9763 Evaluate side-chains 108 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.0870 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 0.0970 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.175135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.143269 restraints weight = 6630.533| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.92 r_work: 0.3485 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6044 Z= 0.153 Angle : 0.594 15.751 8219 Z= 0.303 Chirality : 0.041 0.167 899 Planarity : 0.004 0.038 1013 Dihedral : 4.347 18.293 819 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.22 % Allowed : 11.87 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.31), residues: 738 helix: 1.31 (0.26), residues: 377 sheet: -0.82 (0.46), residues: 114 loop : -1.06 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 218 HIS 0.002 0.001 HIS A 151 PHE 0.017 0.001 PHE A 300 TYR 0.021 0.001 TYR A 137 ARG 0.006 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 318) hydrogen bonds : angle 4.69218 ( 921) SS BOND : bond 0.00142 ( 3) SS BOND : angle 1.21296 ( 6) covalent geometry : bond 0.00353 ( 6041) covalent geometry : angle 0.59315 ( 8213) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.604 Fit side-chains REVERT: L 107 MET cc_start: 0.8287 (mmm) cc_final: 0.8002 (mmt) REVERT: A 212 ASN cc_start: 0.7994 (t0) cc_final: 0.7755 (t0) REVERT: A 388 SER cc_start: 0.8901 (t) cc_final: 0.8301 (p) REVERT: A 441 LEU cc_start: 0.8496 (mp) cc_final: 0.8248 (mm) REVERT: A 498 TYR cc_start: 0.8929 (p90) cc_final: 0.8686 (p90) REVERT: A 567 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7820 (mtt180) outliers start: 14 outliers final: 12 residues processed: 107 average time/residue: 0.2127 time to fit residues: 29.7143 Evaluate side-chains 106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 62 optimal weight: 0.0570 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.176062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.144230 restraints weight = 6685.477| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.94 r_work: 0.3499 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6044 Z= 0.132 Angle : 0.577 14.397 8219 Z= 0.296 Chirality : 0.040 0.167 899 Planarity : 0.004 0.038 1013 Dihedral : 4.285 17.578 819 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.22 % Allowed : 12.97 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.31), residues: 738 helix: 1.40 (0.27), residues: 377 sheet: -0.85 (0.46), residues: 114 loop : -1.03 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 218 HIS 0.005 0.001 HIS H 80 PHE 0.017 0.001 PHE A 300 TYR 0.021 0.001 TYR A 137 ARG 0.007 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 318) hydrogen bonds : angle 4.62668 ( 921) SS BOND : bond 0.00174 ( 3) SS BOND : angle 1.01650 ( 6) covalent geometry : bond 0.00298 ( 6041) covalent geometry : angle 0.57630 ( 8213) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.612 Fit side-chains REVERT: L 107 MET cc_start: 0.8301 (mmm) cc_final: 0.7999 (mmt) REVERT: A 212 ASN cc_start: 0.7936 (t0) cc_final: 0.7719 (t0) REVERT: A 388 SER cc_start: 0.8888 (t) cc_final: 0.8298 (p) REVERT: A 441 LEU cc_start: 0.8476 (mp) cc_final: 0.8218 (mm) REVERT: A 498 TYR cc_start: 0.8904 (p90) cc_final: 0.8666 (p90) REVERT: A 567 ARG cc_start: 0.8219 (mtm-85) cc_final: 0.7776 (mtt180) outliers start: 14 outliers final: 12 residues processed: 107 average time/residue: 0.2119 time to fit residues: 29.5220 Evaluate side-chains 108 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 22 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 4 optimal weight: 0.0970 chunk 72 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 1 optimal weight: 0.0370 chunk 15 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.3256 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.177255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.145403 restraints weight = 6624.642| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.94 r_work: 0.3512 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6044 Z= 0.127 Angle : 0.568 13.337 8219 Z= 0.292 Chirality : 0.040 0.166 899 Planarity : 0.004 0.039 1013 Dihedral : 4.229 17.099 819 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.37 % Allowed : 13.13 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.31), residues: 738 helix: 1.47 (0.27), residues: 377 sheet: -0.81 (0.46), residues: 114 loop : -1.01 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 218 HIS 0.004 0.001 HIS H 80 PHE 0.018 0.001 PHE A 300 TYR 0.022 0.001 TYR A 137 ARG 0.007 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 318) hydrogen bonds : angle 4.57060 ( 921) SS BOND : bond 0.00188 ( 3) SS BOND : angle 0.92791 ( 6) covalent geometry : bond 0.00284 ( 6041) covalent geometry : angle 0.56794 ( 8213) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.762 Fit side-chains REVERT: H 67 ARG cc_start: 0.8574 (ptt90) cc_final: 0.8207 (ptm-80) REVERT: L 107 MET cc_start: 0.8279 (mmm) cc_final: 0.7950 (mmt) REVERT: A 138 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: A 191 PHE cc_start: 0.7314 (m-10) cc_final: 0.7004 (m-10) REVERT: A 388 SER cc_start: 0.8863 (t) cc_final: 0.8280 (p) REVERT: A 441 LEU cc_start: 0.8463 (mp) cc_final: 0.8211 (mm) REVERT: A 498 TYR cc_start: 0.8896 (p90) cc_final: 0.8667 (p90) REVERT: A 567 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7715 (mtt180) outliers start: 15 outliers final: 12 residues processed: 110 average time/residue: 0.2224 time to fit residues: 31.9025 Evaluate side-chains 109 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 46 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.176311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144454 restraints weight = 6649.807| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.94 r_work: 0.3501 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6044 Z= 0.139 Angle : 0.575 12.562 8219 Z= 0.297 Chirality : 0.040 0.162 899 Planarity : 0.004 0.038 1013 Dihedral : 4.236 16.424 819 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.37 % Allowed : 13.29 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.31), residues: 738 helix: 1.44 (0.26), residues: 377 sheet: -0.80 (0.46), residues: 114 loop : -0.93 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 218 HIS 0.004 0.001 HIS H 80 PHE 0.017 0.001 PHE A 300 TYR 0.021 0.001 TYR A 137 ARG 0.007 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 318) hydrogen bonds : angle 4.61810 ( 921) SS BOND : bond 0.00178 ( 3) SS BOND : angle 0.96264 ( 6) covalent geometry : bond 0.00318 ( 6041) covalent geometry : angle 0.57506 ( 8213) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.653 Fit side-chains REVERT: L 107 MET cc_start: 0.8287 (mmm) cc_final: 0.8023 (mmt) REVERT: A 388 SER cc_start: 0.8876 (t) cc_final: 0.8306 (p) REVERT: A 441 LEU cc_start: 0.8428 (mp) cc_final: 0.8179 (mm) REVERT: A 498 TYR cc_start: 0.8874 (p90) cc_final: 0.8655 (p90) REVERT: A 567 ARG cc_start: 0.8207 (mtm-85) cc_final: 0.7723 (mtt180) outliers start: 15 outliers final: 12 residues processed: 106 average time/residue: 0.2436 time to fit residues: 33.4752 Evaluate side-chains 106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 58 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.175913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144223 restraints weight = 6701.959| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.93 r_work: 0.3499 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6044 Z= 0.147 Angle : 0.585 12.267 8219 Z= 0.303 Chirality : 0.041 0.163 899 Planarity : 0.004 0.038 1013 Dihedral : 4.240 16.089 819 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.06 % Allowed : 13.92 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.31), residues: 738 helix: 1.43 (0.26), residues: 377 sheet: -0.77 (0.46), residues: 114 loop : -0.90 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 218 HIS 0.004 0.001 HIS H 80 PHE 0.017 0.001 PHE A 300 TYR 0.021 0.001 TYR A 137 ARG 0.008 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 318) hydrogen bonds : angle 4.64364 ( 921) SS BOND : bond 0.00194 ( 3) SS BOND : angle 0.90740 ( 6) covalent geometry : bond 0.00337 ( 6041) covalent geometry : angle 0.58438 ( 8213) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.587 Fit side-chains REVERT: A 388 SER cc_start: 0.8875 (t) cc_final: 0.8310 (p) REVERT: A 441 LEU cc_start: 0.8399 (mp) cc_final: 0.8176 (mm) REVERT: A 498 TYR cc_start: 0.8873 (p90) cc_final: 0.8651 (p90) outliers start: 13 outliers final: 11 residues processed: 106 average time/residue: 0.2256 time to fit residues: 30.8952 Evaluate side-chains 106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.169864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138086 restraints weight = 6718.437| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.91 r_work: 0.3413 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6044 Z= 0.244 Angle : 0.653 11.924 8219 Z= 0.340 Chirality : 0.044 0.158 899 Planarity : 0.004 0.037 1013 Dihedral : 4.547 17.213 819 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.22 % Allowed : 13.45 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.30), residues: 738 helix: 1.11 (0.26), residues: 374 sheet: -0.95 (0.45), residues: 114 loop : -0.91 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 218 HIS 0.004 0.001 HIS H 80 PHE 0.023 0.002 PHE A 455 TYR 0.016 0.002 TYR A 137 ARG 0.008 0.001 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.04797 ( 318) hydrogen bonds : angle 4.98213 ( 921) SS BOND : bond 0.00228 ( 3) SS BOND : angle 1.23426 ( 6) covalent geometry : bond 0.00583 ( 6041) covalent geometry : angle 0.65211 ( 8213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3853.43 seconds wall clock time: 68 minutes 3.09 seconds (4083.09 seconds total)