Starting phenix.real_space_refine on Sat Apr 4 20:44:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wtj_32788/04_2026/7wtj_32788.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wtj_32788/04_2026/7wtj_32788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wtj_32788/04_2026/7wtj_32788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wtj_32788/04_2026/7wtj_32788.map" model { file = "/net/cci-nas-00/data/ceres_data/7wtj_32788/04_2026/7wtj_32788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wtj_32788/04_2026/7wtj_32788.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2073 2.51 5 N 554 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 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3261 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 878 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 801 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1582 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 12, 'TRANS': 184} Time building chain proxies: 0.87, per 1000 atoms: 0.27 Number of scatterers: 3261 At special positions: 0 Unit cell: (79.18, 82.39, 84.53, 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 14 16.00 O 620 8.00 N 554 7.00 C 2073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 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: 0.21 Conformation dependent library (CDL) restraints added in 120.7 milliseconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 7 sheets defined 6.8% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.954A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.514A pdb=" N ASN E 343 " --> pdb=" O ASP E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.534A pdb=" N ALA E 352 " --> pdb=" O SER E 349 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 349 through 353' Processing helix chain 'E' and resid 364 through 369 removed outlier: 3.837A pdb=" N VAL E 367 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 removed outlier: 3.940A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA E 411 " --> pdb=" O ARG E 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.635A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 60 removed outlier: 3.718A pdb=" N GLY H 57 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL H 117 " --> pdb=" O ALA H 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.797A pdb=" N SER L 64 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.617A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA L 90 " --> pdb=" O TYR L 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 398 through 403 removed outlier: 3.600A pdb=" N ARG E 509 " --> pdb=" O TRP E 436 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474 60 hydrogen bonds defined for protein. 138 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: 0.29 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 524 1.30 - 1.43: 986 1.43 - 1.56: 1826 1.56 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3352 Sorted by residual: bond pdb=" CA SER E 443 " pdb=" CB SER E 443 " ideal model delta sigma weight residual 1.532 1.378 0.154 1.68e-02 3.54e+03 8.41e+01 bond pdb=" CA SER E 438 " pdb=" CB SER E 438 " ideal model delta sigma weight residual 1.524 1.396 0.128 1.62e-02 3.81e+03 6.22e+01 bond pdb=" CA SER E 438 " pdb=" C SER E 438 " ideal model delta sigma weight residual 1.528 1.463 0.065 1.18e-02 7.18e+03 3.07e+01 bond pdb=" C SER E 438 " pdb=" O SER E 438 " ideal model delta sigma weight residual 1.234 1.181 0.053 1.22e-02 6.72e+03 1.88e+01 bond pdb=" C SER E 443 " pdb=" O SER E 443 " ideal model delta sigma weight residual 1.233 1.185 0.049 1.17e-02 7.31e+03 1.72e+01 ... (remaining 3347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 4419 2.13 - 4.26: 113 4.26 - 6.39: 29 6.39 - 8.52: 5 8.52 - 10.65: 2 Bond angle restraints: 4568 Sorted by residual: angle pdb=" C ASP E 442 " pdb=" CA ASP E 442 " pdb=" CB ASP E 442 " ideal model delta sigma weight residual 111.88 101.23 10.65 1.41e+00 5.03e-01 5.71e+01 angle pdb=" C SER E 438 " pdb=" CA SER E 438 " pdb=" CB SER E 438 " ideal model delta sigma weight residual 111.82 102.80 9.02 1.38e+00 5.25e-01 4.27e+01 angle pdb=" O TRP E 436 " pdb=" C TRP E 436 " pdb=" N ASN E 437 " ideal model delta sigma weight residual 123.42 117.37 6.05 1.07e+00 8.73e-01 3.20e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 118.22 -5.62 1.00e+00 1.00e+00 3.15e+01 angle pdb=" CA SER E 443 " pdb=" C SER E 443 " pdb=" O SER E 443 " ideal model delta sigma weight residual 121.38 116.07 5.31 1.06e+00 8.90e-01 2.51e+01 ... (remaining 4563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 1752 17.35 - 34.71: 163 34.71 - 52.06: 32 52.06 - 69.41: 4 69.41 - 86.76: 5 Dihedral angle restraints: 1956 sinusoidal: 740 harmonic: 1216 Sorted by residual: dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 7.19 85.81 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 150.75 -57.75 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CA CYS E 391 " pdb=" C CYS E 391 " pdb=" N PHE E 392 " pdb=" CA PHE E 392 " ideal model delta harmonic sigma weight residual -180.00 -149.70 -30.30 0 5.00e+00 4.00e-02 3.67e+01 ... (remaining 1953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 390 0.057 - 0.113: 79 0.113 - 0.170: 10 0.170 - 0.227: 4 0.227 - 0.283: 2 Chirality restraints: 485 Sorted by residual: chirality pdb=" CA ASP H 55 " pdb=" N ASP H 55 " pdb=" C ASP H 55 " pdb=" CB ASP H 55 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ASN E 439 " pdb=" N ASN E 439 " pdb=" C ASN E 439 " pdb=" CB ASN E 439 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA LYS E 440 " pdb=" N LYS E 440 " pdb=" C LYS E 440 " pdb=" CB LYS E 440 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 482 not shown) Planarity restraints: 593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 497 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.74e+00 pdb=" C PHE E 497 " -0.054 2.00e-02 2.50e+03 pdb=" O PHE E 497 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG E 498 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 54 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C GLY H 54 " 0.053 2.00e-02 2.50e+03 pdb=" O GLY H 54 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP H 55 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 441 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C LEU E 441 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU E 441 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP E 442 " 0.015 2.00e-02 2.50e+03 ... (remaining 590 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 649 2.77 - 3.31: 2916 3.31 - 3.84: 4813 3.84 - 4.37: 5398 4.37 - 4.90: 9724 Nonbonded interactions: 23500 Sorted by model distance: nonbonded pdb=" OG1 THR L 5 " pdb=" OG SER L 23 " model vdw 2.242 3.040 nonbonded pdb=" NH1 ARG L 62 " pdb=" O SER L 77 " model vdw 2.292 3.120 nonbonded pdb=" O VAL E 367 " pdb=" ND2 ASN E 370 " model vdw 2.350 3.120 nonbonded pdb=" O ASP E 442 " pdb=" CB ASP E 442 " model vdw 2.369 2.752 nonbonded pdb=" O GLY L 78 " pdb=" NE ARG L 80 " model vdw 2.375 3.120 ... (remaining 23495 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: 1.850 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.780 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 3358 Z= 0.386 Angle : 0.858 10.652 4580 Z= 0.523 Chirality : 0.052 0.283 485 Planarity : 0.006 0.047 593 Dihedral : 13.858 86.764 1170 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.58 % Allowed : 0.29 % Favored : 99.14 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.40), residues: 418 helix: -3.24 (1.01), residues: 13 sheet: -0.37 (0.53), residues: 104 loop : -1.93 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 55 TYR 0.009 0.001 TYR E 495 PHE 0.009 0.001 PHE E 377 TRP 0.009 0.001 TRP H 111 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00597 ( 3352) covalent geometry : angle 0.84947 ( 4568) SS BOND : bond 0.00206 ( 6) SS BOND : angle 2.49092 ( 12) hydrogen bonds : bond 0.23574 ( 60) hydrogen bonds : angle 11.28832 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.072 Fit side-chains REVERT: H 82 GLU cc_start: 0.7106 (mp0) cc_final: 0.6621 (mp0) REVERT: E 441 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8301 (mt) outliers start: 2 outliers final: 1 residues processed: 87 average time/residue: 0.0532 time to fit residues: 5.6584 Evaluate side-chains 76 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 37 optimal weight: 0.0570 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105046 restraints weight = 6467.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106190 restraints weight = 4651.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106901 restraints weight = 3828.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108267 restraints weight = 3299.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108714 restraints weight = 2790.453| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 3358 Z= 0.116 Angle : 0.617 7.893 4580 Z= 0.316 Chirality : 0.045 0.153 485 Planarity : 0.004 0.047 593 Dihedral : 4.824 24.762 469 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.40), residues: 418 helix: -3.59 (0.83), residues: 19 sheet: 0.08 (0.53), residues: 102 loop : -2.00 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 62 TYR 0.007 0.001 TYR L 50 PHE 0.024 0.001 PHE H 64 TRP 0.014 0.001 TRP H 111 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3352) covalent geometry : angle 0.60746 ( 4568) SS BOND : bond 0.00128 ( 6) SS BOND : angle 2.18133 ( 12) hydrogen bonds : bond 0.03434 ( 60) hydrogen bonds : angle 7.70057 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.129 Fit side-chains REVERT: H 55 ASP cc_start: 0.8651 (p0) cc_final: 0.8098 (p0) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0479 time to fit residues: 5.1606 Evaluate side-chains 72 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.124466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103061 restraints weight = 6530.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.103349 restraints weight = 5163.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104362 restraints weight = 4296.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105285 restraints weight = 3510.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105687 restraints weight = 3170.143| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 3358 Z= 0.129 Angle : 0.622 8.107 4580 Z= 0.316 Chirality : 0.045 0.163 485 Planarity : 0.005 0.048 593 Dihedral : 4.884 24.579 469 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.39), residues: 418 helix: -3.39 (1.01), residues: 13 sheet: 0.08 (0.51), residues: 107 loop : -1.98 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 67 TYR 0.007 0.001 TYR L 50 PHE 0.005 0.001 PHE H 108 TRP 0.008 0.001 TRP H 111 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3352) covalent geometry : angle 0.61043 ( 4568) SS BOND : bond 0.00237 ( 6) SS BOND : angle 2.37252 ( 12) hydrogen bonds : bond 0.03370 ( 60) hydrogen bonds : angle 6.85676 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.140 Fit side-chains REVERT: H 55 ASP cc_start: 0.8774 (p0) cc_final: 0.8284 (p0) REVERT: E 389 ASP cc_start: 0.6663 (p0) cc_final: 0.6328 (p0) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0613 time to fit residues: 6.5920 Evaluate side-chains 74 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.124375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100654 restraints weight = 6441.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.102973 restraints weight = 4535.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104724 restraints weight = 3525.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.105868 restraints weight = 2915.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.106637 restraints weight = 2549.362| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 3358 Z= 0.124 Angle : 0.617 8.098 4580 Z= 0.314 Chirality : 0.045 0.159 485 Planarity : 0.004 0.049 593 Dihedral : 4.859 26.762 469 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.39), residues: 418 helix: -2.69 (1.33), residues: 13 sheet: 0.29 (0.52), residues: 102 loop : -1.97 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 466 TYR 0.013 0.001 TYR L 37 PHE 0.014 0.001 PHE H 64 TRP 0.008 0.001 TRP H 107 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 3352) covalent geometry : angle 0.60449 ( 4568) SS BOND : bond 0.00205 ( 6) SS BOND : angle 2.44347 ( 12) hydrogen bonds : bond 0.03179 ( 60) hydrogen bonds : angle 6.57047 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.118 Fit side-chains REVERT: H 109 ASP cc_start: 0.7049 (m-30) cc_final: 0.6776 (m-30) REVERT: E 389 ASP cc_start: 0.6270 (p0) cc_final: 0.5955 (p0) REVERT: E 424 LYS cc_start: 0.8136 (ptpt) cc_final: 0.7919 (ptmt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0520 time to fit residues: 5.6539 Evaluate side-chains 70 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 0.0470 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.101527 restraints weight = 6395.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103898 restraints weight = 4477.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105669 restraints weight = 3434.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106704 restraints weight = 2819.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107687 restraints weight = 2467.203| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3358 Z= 0.115 Angle : 0.620 8.570 4580 Z= 0.311 Chirality : 0.045 0.159 485 Planarity : 0.005 0.048 593 Dihedral : 4.913 27.192 469 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.39), residues: 418 helix: -2.63 (1.37), residues: 13 sheet: 0.08 (0.50), residues: 107 loop : -1.89 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 98 TYR 0.016 0.001 TYR L 50 PHE 0.015 0.001 PHE H 64 TRP 0.008 0.001 TRP H 111 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3352) covalent geometry : angle 0.60824 ( 4568) SS BOND : bond 0.00194 ( 6) SS BOND : angle 2.39653 ( 12) hydrogen bonds : bond 0.03106 ( 60) hydrogen bonds : angle 6.37110 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: E 424 LYS cc_start: 0.8182 (ptpt) cc_final: 0.7953 (ptmt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0540 time to fit residues: 5.3718 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.120911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099743 restraints weight = 6491.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100760 restraints weight = 4658.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101674 restraints weight = 3721.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102943 restraints weight = 3087.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.103151 restraints weight = 2639.097| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 3358 Z= 0.231 Angle : 0.751 9.140 4580 Z= 0.387 Chirality : 0.049 0.172 485 Planarity : 0.006 0.071 593 Dihedral : 5.690 28.101 469 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.35 % Favored : 85.65 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.39), residues: 418 helix: -2.77 (1.08), residues: 19 sheet: -0.05 (0.52), residues: 100 loop : -2.13 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 466 TYR 0.018 0.002 TYR L 50 PHE 0.029 0.002 PHE E 374 TRP 0.012 0.002 TRP L 101 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 3352) covalent geometry : angle 0.73493 ( 4568) SS BOND : bond 0.00245 ( 6) SS BOND : angle 3.09399 ( 12) hydrogen bonds : bond 0.03743 ( 60) hydrogen bonds : angle 6.84897 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.097 Fit side-chains REVERT: H 11 VAL cc_start: 0.9126 (t) cc_final: 0.8915 (p) REVERT: H 70 LEU cc_start: 0.9178 (tp) cc_final: 0.8944 (tt) REVERT: E 389 ASP cc_start: 0.6684 (p0) cc_final: 0.6450 (p0) REVERT: E 424 LYS cc_start: 0.8280 (ptpt) cc_final: 0.8029 (ptmt) REVERT: E 474 GLN cc_start: 0.7436 (tt0) cc_final: 0.7172 (mt0) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0500 time to fit residues: 5.3195 Evaluate side-chains 69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.104337 restraints weight = 6376.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104889 restraints weight = 4610.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106097 restraints weight = 3779.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106547 restraints weight = 3253.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107327 restraints weight = 2982.318| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3358 Z= 0.115 Angle : 0.652 7.528 4580 Z= 0.327 Chirality : 0.046 0.175 485 Planarity : 0.004 0.050 593 Dihedral : 5.225 32.521 469 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.39), residues: 418 helix: -3.02 (1.15), residues: 13 sheet: -0.00 (0.50), residues: 107 loop : -1.94 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.013 0.001 TYR L 50 PHE 0.016 0.001 PHE H 64 TRP 0.013 0.001 TRP L 92 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3352) covalent geometry : angle 0.63950 ( 4568) SS BOND : bond 0.00230 ( 6) SS BOND : angle 2.57096 ( 12) hydrogen bonds : bond 0.03058 ( 60) hydrogen bonds : angle 6.35624 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.105 Fit side-chains REVERT: H 70 LEU cc_start: 0.9085 (tp) cc_final: 0.8867 (tt) REVERT: E 389 ASP cc_start: 0.6428 (p0) cc_final: 0.6083 (p0) REVERT: E 424 LYS cc_start: 0.8205 (ptpt) cc_final: 0.7982 (ptmt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0483 time to fit residues: 4.8793 Evaluate side-chains 72 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 0.0010 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.125525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105344 restraints weight = 6462.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105688 restraints weight = 4821.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106600 restraints weight = 4061.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107079 restraints weight = 3472.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107374 restraints weight = 3220.594| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 3358 Z= 0.121 Angle : 0.661 9.176 4580 Z= 0.331 Chirality : 0.046 0.179 485 Planarity : 0.005 0.051 593 Dihedral : 5.224 34.988 469 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.39), residues: 418 helix: -2.90 (1.23), residues: 13 sheet: 0.20 (0.50), residues: 103 loop : -1.95 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 509 TYR 0.013 0.001 TYR L 50 PHE 0.020 0.001 PHE E 374 TRP 0.018 0.002 TRP L 101 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3352) covalent geometry : angle 0.64701 ( 4568) SS BOND : bond 0.00243 ( 6) SS BOND : angle 2.74852 ( 12) hydrogen bonds : bond 0.03095 ( 60) hydrogen bonds : angle 6.11078 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.118 Fit side-chains REVERT: H 70 LEU cc_start: 0.9131 (tp) cc_final: 0.8923 (tt) REVERT: E 389 ASP cc_start: 0.6345 (p0) cc_final: 0.6101 (p0) REVERT: E 424 LYS cc_start: 0.8213 (ptpt) cc_final: 0.7992 (ptmt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0450 time to fit residues: 4.5875 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.0010 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.125744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105241 restraints weight = 6347.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105781 restraints weight = 4925.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107066 restraints weight = 3966.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107586 restraints weight = 3246.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108183 restraints weight = 2999.640| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 3358 Z= 0.122 Angle : 0.658 8.324 4580 Z= 0.329 Chirality : 0.046 0.166 485 Planarity : 0.005 0.052 593 Dihedral : 5.189 34.605 469 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.39), residues: 418 helix: -2.92 (1.20), residues: 13 sheet: 0.20 (0.50), residues: 103 loop : -1.91 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 509 TYR 0.012 0.001 TYR L 50 PHE 0.016 0.001 PHE H 64 TRP 0.012 0.001 TRP L 92 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3352) covalent geometry : angle 0.64481 ( 4568) SS BOND : bond 0.00264 ( 6) SS BOND : angle 2.66094 ( 12) hydrogen bonds : bond 0.03028 ( 60) hydrogen bonds : angle 6.05324 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.133 Fit side-chains REVERT: H 70 LEU cc_start: 0.9141 (tp) cc_final: 0.8918 (tt) REVERT: E 389 ASP cc_start: 0.6397 (p0) cc_final: 0.6136 (p0) REVERT: E 424 LYS cc_start: 0.8239 (ptpt) cc_final: 0.8003 (ptmt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0554 time to fit residues: 5.4493 Evaluate side-chains 65 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.0770 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.125863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105542 restraints weight = 6482.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106106 restraints weight = 5063.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107253 restraints weight = 4026.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107782 restraints weight = 3331.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108377 restraints weight = 3083.696| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 3358 Z= 0.118 Angle : 0.650 8.403 4580 Z= 0.324 Chirality : 0.046 0.165 485 Planarity : 0.005 0.052 593 Dihedral : 5.155 34.579 469 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.39), residues: 418 helix: -3.25 (1.03), residues: 13 sheet: 0.22 (0.50), residues: 103 loop : -1.91 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 509 TYR 0.013 0.001 TYR L 50 PHE 0.017 0.001 PHE H 64 TRP 0.010 0.001 TRP H 111 HIS 0.005 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3352) covalent geometry : angle 0.63690 ( 4568) SS BOND : bond 0.00253 ( 6) SS BOND : angle 2.59564 ( 12) hydrogen bonds : bond 0.02979 ( 60) hydrogen bonds : angle 5.99872 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.133 Fit side-chains REVERT: H 70 LEU cc_start: 0.9106 (tp) cc_final: 0.8870 (tt) REVERT: E 389 ASP cc_start: 0.6379 (p0) cc_final: 0.6146 (p0) REVERT: E 424 LYS cc_start: 0.8225 (ptpt) cc_final: 0.7978 (ptmt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0576 time to fit residues: 5.5444 Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.123746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103202 restraints weight = 6506.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103778 restraints weight = 5255.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104773 restraints weight = 4236.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105312 restraints weight = 3507.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106138 restraints weight = 3243.097| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3358 Z= 0.158 Angle : 0.695 8.444 4580 Z= 0.349 Chirality : 0.047 0.170 485 Planarity : 0.005 0.052 593 Dihedral : 5.467 36.040 469 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.40), residues: 418 helix: -3.19 (0.92), residues: 19 sheet: -0.05 (0.48), residues: 118 loop : -2.01 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 62 TYR 0.012 0.001 TYR L 50 PHE 0.020 0.002 PHE H 64 TRP 0.013 0.002 TRP L 36 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 3352) covalent geometry : angle 0.68024 ( 4568) SS BOND : bond 0.00200 ( 6) SS BOND : angle 2.82013 ( 12) hydrogen bonds : bond 0.03164 ( 60) hydrogen bonds : angle 6.19825 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 780.76 seconds wall clock time: 14 minutes 2.29 seconds (842.29 seconds total)