Starting phenix.real_space_refine on Sat Apr 26 19:28:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9js4_61766/04_2025/9js4_61766.cif Found real_map, /net/cci-nas-00/data/ceres_data/9js4_61766/04_2025/9js4_61766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9js4_61766/04_2025/9js4_61766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9js4_61766/04_2025/9js4_61766.map" model { file = "/net/cci-nas-00/data/ceres_data/9js4_61766/04_2025/9js4_61766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9js4_61766/04_2025/9js4_61766.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2065 2.51 5 N 544 2.21 5 O 620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3244 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "B" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 854 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain breaks: 1 Chain: "C" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1574 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 12, 'TRANS': 183} Time building chain proxies: 3.47, per 1000 atoms: 1.07 Number of scatterers: 3244 At special positions: 0 Unit cell: (66, 73.7, 101.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 620 8.00 N 544 7.00 C 2065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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: 0.77 Conformation dependent library (CDL) restraints added in 409.5 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 9.6% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.588A pdb=" N ILE A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.509A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 372 removed outlier: 4.562A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.619A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.957A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.905A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 4.019A pdb=" N THR A 5 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 90 removed outlier: 3.589A pdb=" N HIS A 90 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR A 100 " --> pdb=" O HIS A 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 22 removed outlier: 3.679A pdb=" N THR B 68 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.832A pdb=" N TYR B 58 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 50 " --> pdb=" O TYR B 58 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 92 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.111A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.692A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) 59 hydrogen bonds defined for protein. 147 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: 0.77 Time building geometry restraints manager: 0.94 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: 1041 1.34 - 1.46: 861 1.46 - 1.58: 1409 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3329 Sorted by residual: bond pdb=" CA VAL B 63 " pdb=" CB VAL B 63 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 1.04e+00 bond pdb=" CG PRO C 384 " pdb=" CD PRO C 384 " ideal model delta sigma weight residual 1.503 1.533 -0.030 3.40e-02 8.65e+02 7.77e-01 bond pdb=" CB ASP C 428 " pdb=" CG ASP C 428 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.62e-01 bond pdb=" CB ASN A 31 " pdb=" CG ASN A 31 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.29e-01 bond pdb=" CA ASN A 31 " pdb=" CB ASN A 31 " ideal model delta sigma weight residual 1.533 1.546 -0.013 1.66e-02 3.63e+03 5.73e-01 ... (remaining 3324 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 4289 1.22 - 2.44: 191 2.44 - 3.67: 41 3.67 - 4.89: 11 4.89 - 6.11: 2 Bond angle restraints: 4534 Sorted by residual: angle pdb=" CA CYS C 361 " pdb=" CB CYS C 361 " pdb=" SG CYS C 361 " ideal model delta sigma weight residual 114.40 120.51 -6.11 2.30e+00 1.89e-01 7.06e+00 angle pdb=" CA TYR A 91 " pdb=" CB TYR A 91 " pdb=" CG TYR A 91 " ideal model delta sigma weight residual 113.90 118.45 -4.55 1.80e+00 3.09e-01 6.39e+00 angle pdb=" C SER A 30 " pdb=" N ASN A 31 " pdb=" CA ASN A 31 " ideal model delta sigma weight residual 123.91 127.83 -3.92 1.66e+00 3.63e-01 5.56e+00 angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 116.81 -4.47 2.04e+00 2.40e-01 4.80e+00 angle pdb=" CA ASN A 31 " pdb=" CB ASN A 31 " pdb=" CG ASN A 31 " ideal model delta sigma weight residual 112.60 114.76 -2.16 1.00e+00 1.00e+00 4.65e+00 ... (remaining 4529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.78: 1728 14.78 - 29.56: 174 29.56 - 44.34: 51 44.34 - 59.12: 6 59.12 - 73.90: 5 Dihedral angle restraints: 1964 sinusoidal: 760 harmonic: 1204 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 166.90 -73.90 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 163.36 -70.36 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" CA CYS C 361 " pdb=" C CYS C 361 " pdb=" N VAL C 362 " pdb=" CA VAL C 362 " ideal model delta harmonic sigma weight residual 180.00 148.04 31.96 0 5.00e+00 4.00e-02 4.09e+01 ... (remaining 1961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 262 0.027 - 0.054: 129 0.054 - 0.080: 57 0.080 - 0.107: 30 0.107 - 0.134: 12 Chirality restraints: 490 Sorted by residual: chirality pdb=" CA VAL B 50 " pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CB VAL B 50 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ASN A 31 " pdb=" N ASN A 31 " pdb=" C ASN A 31 " pdb=" CB ASN A 31 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 487 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 383 " -0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO C 384 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 384 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 384 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO C 463 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 52 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO B 53 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 53 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 53 " 0.019 5.00e-02 4.00e+02 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 913 2.81 - 3.33: 2664 3.33 - 3.85: 4632 3.85 - 4.38: 4990 4.38 - 4.90: 9122 Nonbonded interactions: 22321 Sorted by model distance: nonbonded pdb=" OG1 THR B 28 " pdb=" O ALA C 475 " model vdw 2.286 3.040 nonbonded pdb=" ND2 ASN A 96 " pdb=" OD2 ASP C 405 " model vdw 2.331 3.120 nonbonded pdb=" NE2 GLN A 38 " pdb=" O LYS A 39 " model vdw 2.380 3.120 nonbonded pdb=" NH1 ARG B 38 " pdb=" OD1 ASP B 89 " model vdw 2.403 3.120 nonbonded pdb=" NH2 ARG C 454 " pdb=" OD2 ASP C 467 " model vdw 2.418 3.120 ... (remaining 22316 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.730 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 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 : 0.002 0.030 3335 Z= 0.118 Angle : 0.624 6.111 4546 Z= 0.333 Chirality : 0.044 0.134 490 Planarity : 0.006 0.089 589 Dihedral : 12.564 73.350 1184 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.81 (0.38), residues: 409 helix: -3.08 (0.79), residues: 20 sheet: -0.42 (0.47), residues: 120 loop : -1.48 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS C 519 PHE 0.010 0.001 PHE B 67 TYR 0.014 0.001 TYR C 501 ARG 0.003 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.18371 ( 59) hydrogen bonds : angle 8.83364 ( 147) SS BOND : bond 0.00454 ( 6) SS BOND : angle 2.16759 ( 12) covalent geometry : bond 0.00249 ( 3329) covalent geometry : angle 0.61521 ( 4534) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.384 Fit side-chains REVERT: B 84 SER cc_start: 0.7991 (t) cc_final: 0.7750 (t) REVERT: C 405 ASP cc_start: 0.7173 (t70) cc_final: 0.6891 (t0) REVERT: C 489 TYR cc_start: 0.6868 (m-10) cc_final: 0.6433 (m-80) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1147 time to fit residues: 8.7471 Evaluate side-chains 47 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.170334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.156381 restraints weight = 6433.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.158776 restraints weight = 4450.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.160539 restraints weight = 3350.216| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3335 Z= 0.130 Angle : 0.618 4.880 4546 Z= 0.326 Chirality : 0.046 0.168 490 Planarity : 0.005 0.059 589 Dihedral : 5.390 27.690 461 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.41 % Allowed : 9.01 % Favored : 89.58 % 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: -1.82 (0.38), residues: 409 helix: -2.97 (0.84), residues: 20 sheet: -0.38 (0.48), residues: 113 loop : -1.51 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.004 0.001 HIS C 519 PHE 0.011 0.001 PHE C 400 TYR 0.015 0.002 TYR C 489 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 59) hydrogen bonds : angle 7.39103 ( 147) SS BOND : bond 0.00471 ( 6) SS BOND : angle 2.03592 ( 12) covalent geometry : bond 0.00294 ( 3329) covalent geometry : angle 0.60947 ( 4534) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.382 Fit side-chains REVERT: B 84 SER cc_start: 0.7990 (t) cc_final: 0.7734 (t) REVERT: C 465 GLU cc_start: 0.5304 (pm20) cc_final: 0.5076 (pm20) outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 0.1176 time to fit residues: 9.0143 Evaluate side-chains 50 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 333 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.168408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.153315 restraints weight = 6402.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.155913 restraints weight = 4339.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.157885 restraints weight = 3228.374| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3335 Z= 0.140 Angle : 0.617 5.742 4546 Z= 0.327 Chirality : 0.046 0.166 490 Planarity : 0.005 0.049 589 Dihedral : 5.378 20.207 461 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.54 % Allowed : 12.11 % Favored : 85.35 % 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: -1.80 (0.39), residues: 409 helix: -2.61 (0.92), residues: 20 sheet: -0.48 (0.48), residues: 117 loop : -1.47 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.004 0.002 HIS C 519 PHE 0.011 0.002 PHE C 400 TYR 0.013 0.002 TYR C 489 ARG 0.003 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04449 ( 59) hydrogen bonds : angle 7.14896 ( 147) SS BOND : bond 0.00451 ( 6) SS BOND : angle 1.25808 ( 12) covalent geometry : bond 0.00318 ( 3329) covalent geometry : angle 0.61433 ( 4534) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.357 Fit side-chains REVERT: B 84 SER cc_start: 0.7976 (t) cc_final: 0.7730 (t) outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 0.1384 time to fit residues: 9.1502 Evaluate side-chains 46 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 438 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.0470 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN 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 = 0.169641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.154684 restraints weight = 6546.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.157399 restraints weight = 4370.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.159426 restraints weight = 3207.037| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3335 Z= 0.119 Angle : 0.585 6.519 4546 Z= 0.309 Chirality : 0.045 0.164 490 Planarity : 0.005 0.045 589 Dihedral : 5.262 19.802 461 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.82 % Allowed : 11.83 % Favored : 85.35 % 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: -1.77 (0.39), residues: 409 helix: -2.29 (1.05), residues: 20 sheet: -0.42 (0.50), residues: 110 loop : -1.48 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 PHE 0.009 0.001 PHE C 400 TYR 0.011 0.001 TYR C 501 ARG 0.002 0.000 ARG C 466 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 59) hydrogen bonds : angle 6.95432 ( 147) SS BOND : bond 0.00415 ( 6) SS BOND : angle 1.43568 ( 12) covalent geometry : bond 0.00268 ( 3329) covalent geometry : angle 0.58075 ( 4534) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.374 Fit side-chains REVERT: B 84 SER cc_start: 0.7972 (t) cc_final: 0.7731 (t) outliers start: 10 outliers final: 7 residues processed: 51 average time/residue: 0.1046 time to fit residues: 7.3260 Evaluate side-chains 48 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 438 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.166334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.150995 restraints weight = 6526.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.153717 restraints weight = 4355.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.155762 restraints weight = 3200.825| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3335 Z= 0.166 Angle : 0.642 5.574 4546 Z= 0.341 Chirality : 0.047 0.164 490 Planarity : 0.005 0.042 589 Dihedral : 5.693 22.810 461 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.25 % Allowed : 12.96 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.93 (0.40), residues: 409 helix: -2.63 (1.04), residues: 21 sheet: -0.64 (0.50), residues: 116 loop : -1.52 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 436 HIS 0.004 0.002 HIS C 519 PHE 0.014 0.002 PHE C 400 TYR 0.016 0.002 TYR A 49 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04574 ( 59) hydrogen bonds : angle 7.05031 ( 147) SS BOND : bond 0.00372 ( 6) SS BOND : angle 1.74082 ( 12) covalent geometry : bond 0.00380 ( 3329) covalent geometry : angle 0.63663 ( 4534) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.346 Fit side-chains REVERT: B 84 SER cc_start: 0.7960 (t) cc_final: 0.7735 (t) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.1006 time to fit residues: 6.7821 Evaluate side-chains 45 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 438 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 1 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.169995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.155090 restraints weight = 6551.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.157840 restraints weight = 4322.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.159893 restraints weight = 3144.762| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3335 Z= 0.111 Angle : 0.582 4.746 4546 Z= 0.307 Chirality : 0.044 0.161 490 Planarity : 0.004 0.042 589 Dihedral : 5.230 20.876 461 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.54 % Allowed : 14.37 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.86 (0.39), residues: 409 helix: -2.71 (0.98), residues: 21 sheet: -0.58 (0.49), residues: 110 loop : -1.46 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 PHE 0.008 0.001 PHE C 400 TYR 0.011 0.001 TYR A 49 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 59) hydrogen bonds : angle 6.75563 ( 147) SS BOND : bond 0.00279 ( 6) SS BOND : angle 1.52892 ( 12) covalent geometry : bond 0.00249 ( 3329) covalent geometry : angle 0.57756 ( 4534) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.343 Fit side-chains REVERT: B 84 SER cc_start: 0.7951 (t) cc_final: 0.7713 (t) outliers start: 9 outliers final: 7 residues processed: 50 average time/residue: 0.0994 time to fit residues: 6.8090 Evaluate side-chains 47 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 438 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 31 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.169610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.155059 restraints weight = 6443.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.157738 restraints weight = 4304.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.159719 restraints weight = 3155.795| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3335 Z= 0.118 Angle : 0.606 7.220 4546 Z= 0.320 Chirality : 0.045 0.180 490 Planarity : 0.004 0.041 589 Dihedral : 5.192 20.513 461 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.10 % Allowed : 14.65 % Favored : 82.25 % 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: -1.86 (0.40), residues: 409 helix: -2.84 (0.95), residues: 21 sheet: -0.59 (0.49), residues: 110 loop : -1.44 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 PHE 0.010 0.001 PHE C 429 TYR 0.012 0.001 TYR C 489 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 59) hydrogen bonds : angle 6.58827 ( 147) SS BOND : bond 0.00310 ( 6) SS BOND : angle 1.74927 ( 12) covalent geometry : bond 0.00261 ( 3329) covalent geometry : angle 0.60042 ( 4534) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.289 Fit side-chains REVERT: B 84 SER cc_start: 0.7915 (t) cc_final: 0.7694 (t) REVERT: C 386 LYS cc_start: 0.3340 (mmtt) cc_final: 0.2204 (ttpt) REVERT: C 465 GLU cc_start: 0.5397 (pm20) cc_final: 0.5180 (pm20) outliers start: 11 outliers final: 8 residues processed: 52 average time/residue: 0.1004 time to fit residues: 6.9904 Evaluate side-chains 51 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 438 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 0.0060 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.168125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.153714 restraints weight = 6477.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.156304 restraints weight = 4344.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.158218 restraints weight = 3212.659| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3335 Z= 0.144 Angle : 0.639 7.305 4546 Z= 0.338 Chirality : 0.045 0.173 490 Planarity : 0.005 0.040 589 Dihedral : 5.366 19.655 461 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.82 % Allowed : 14.37 % Favored : 82.82 % 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: -1.93 (0.40), residues: 409 helix: -2.98 (0.92), residues: 21 sheet: -0.57 (0.50), residues: 110 loop : -1.51 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.004 0.001 HIS C 519 PHE 0.013 0.001 PHE C 429 TYR 0.013 0.002 TYR A 49 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 59) hydrogen bonds : angle 6.65160 ( 147) SS BOND : bond 0.00383 ( 6) SS BOND : angle 1.95963 ( 12) covalent geometry : bond 0.00326 ( 3329) covalent geometry : angle 0.63174 ( 4534) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.380 Fit side-chains REVERT: B 84 SER cc_start: 0.7928 (t) cc_final: 0.7707 (t) REVERT: C 386 LYS cc_start: 0.3195 (mmtt) cc_final: 0.2121 (ttmt) REVERT: C 465 GLU cc_start: 0.5456 (pm20) cc_final: 0.5245 (pm20) outliers start: 10 outliers final: 8 residues processed: 51 average time/residue: 0.1087 time to fit residues: 7.5266 Evaluate side-chains 51 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 438 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.168974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.154285 restraints weight = 6538.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.156911 restraints weight = 4332.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.158926 restraints weight = 3187.037| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3335 Z= 0.127 Angle : 0.627 7.244 4546 Z= 0.331 Chirality : 0.045 0.172 490 Planarity : 0.005 0.041 589 Dihedral : 5.240 19.413 461 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.10 % Allowed : 14.93 % Favored : 81.97 % 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: -1.92 (0.40), residues: 409 helix: -3.07 (0.88), residues: 21 sheet: -0.55 (0.50), residues: 110 loop : -1.50 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 PHE 0.011 0.001 PHE C 429 TYR 0.012 0.001 TYR A 49 ARG 0.001 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 59) hydrogen bonds : angle 6.60141 ( 147) SS BOND : bond 0.00285 ( 6) SS BOND : angle 1.91911 ( 12) covalent geometry : bond 0.00287 ( 3329) covalent geometry : angle 0.61971 ( 4534) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.337 Fit side-chains REVERT: B 84 SER cc_start: 0.7970 (t) cc_final: 0.7726 (t) REVERT: C 375 PHE cc_start: 0.6886 (OUTLIER) cc_final: 0.6458 (t80) REVERT: C 386 LYS cc_start: 0.3130 (mmtt) cc_final: 0.2132 (ttmt) REVERT: C 465 GLU cc_start: 0.5512 (pm20) cc_final: 0.5304 (pm20) outliers start: 11 outliers final: 9 residues processed: 50 average time/residue: 0.0991 time to fit residues: 6.7940 Evaluate side-chains 51 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 438 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.168411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154274 restraints weight = 6420.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.156763 restraints weight = 4354.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.158633 restraints weight = 3240.585| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3335 Z= 0.138 Angle : 0.644 7.313 4546 Z= 0.340 Chirality : 0.046 0.172 490 Planarity : 0.005 0.041 589 Dihedral : 5.329 19.096 461 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.10 % Allowed : 15.21 % Favored : 81.69 % 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: -1.82 (0.40), residues: 409 helix: -2.53 (1.18), residues: 14 sheet: -0.41 (0.53), residues: 103 loop : -1.53 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 PHE 0.014 0.001 PHE C 429 TYR 0.013 0.002 TYR A 49 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 59) hydrogen bonds : angle 6.63046 ( 147) SS BOND : bond 0.00364 ( 6) SS BOND : angle 2.02305 ( 12) covalent geometry : bond 0.00314 ( 3329) covalent geometry : angle 0.63615 ( 4534) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.381 Fit side-chains REVERT: B 84 SER cc_start: 0.7962 (t) cc_final: 0.7719 (t) REVERT: C 375 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6355 (t80) REVERT: C 386 LYS cc_start: 0.3309 (mmtt) cc_final: 0.2189 (ttmt) REVERT: C 420 ASP cc_start: 0.8366 (t70) cc_final: 0.8074 (t0) outliers start: 11 outliers final: 9 residues processed: 51 average time/residue: 0.1078 time to fit residues: 7.5987 Evaluate side-chains 52 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 438 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 36 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.169263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.154700 restraints weight = 6428.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.157334 restraints weight = 4289.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.159294 restraints weight = 3144.781| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3335 Z= 0.127 Angle : 0.630 7.302 4546 Z= 0.333 Chirality : 0.045 0.170 490 Planarity : 0.004 0.041 589 Dihedral : 5.234 20.441 461 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.10 % Allowed : 15.21 % Favored : 81.69 % 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: -1.80 (0.40), residues: 409 helix: -2.90 (1.07), residues: 15 sheet: -0.36 (0.53), residues: 103 loop : -1.50 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 PHE 0.013 0.001 PHE C 429 TYR 0.013 0.001 TYR A 49 ARG 0.001 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 59) hydrogen bonds : angle 6.54475 ( 147) SS BOND : bond 0.00321 ( 6) SS BOND : angle 1.92003 ( 12) covalent geometry : bond 0.00287 ( 3329) covalent geometry : angle 0.62326 ( 4534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1529.17 seconds wall clock time: 27 minutes 13.64 seconds (1633.64 seconds total)