Starting phenix.real_space_refine on Tue Mar 3 11:04:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm0_27522/03_2026/8dm0_27522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm0_27522/03_2026/8dm0_27522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm0_27522/03_2026/8dm0_27522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm0_27522/03_2026/8dm0_27522.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm0_27522/03_2026/8dm0_27522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm0_27522/03_2026/8dm0_27522.cif" } resolution = 3.21 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= 0.014 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 13 5.16 5 C 1582 2.51 5 N 414 2.21 5 O 471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2480 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.69, per 1000 atoms: 0.28 Number of scatterers: 2480 At special positions: 0 Unit cell: (68, 81, 70, 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 13 16.00 O 471 8.00 N 414 7.00 C 1582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " 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 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.21 Conformation dependent library (CDL) restraints added in 115.4 milliseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 572 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 5 sheets defined 13.4% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.552A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.078A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.276A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.512A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.647A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.710A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.129A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 183 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: 0.38 Time building geometry restraints manager: 0.30 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: 786 1.34 - 1.46: 647 1.46 - 1.58: 1097 1.58 - 1.69: 1 1.69 - 1.81: 16 Bond restraints: 2547 Sorted by residual: bond pdb=" CB PRO H 14 " pdb=" CG PRO H 14 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.83e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.78e+00 bond pdb=" N ASP H 107 " pdb=" CA ASP H 107 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.04e+00 bond pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.72e+00 bond pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.40e+00 ... (remaining 2542 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 3318 2.25 - 4.50: 126 4.50 - 6.74: 16 6.74 - 8.99: 4 8.99 - 11.24: 2 Bond angle restraints: 3466 Sorted by residual: angle pdb=" C TYR C 505 " pdb=" N GLN C 506 " pdb=" CA GLN C 506 " ideal model delta sigma weight residual 120.68 131.92 -11.24 1.52e+00 4.33e-01 5.47e+01 angle pdb=" CA PRO H 14 " pdb=" N PRO H 14 " pdb=" CD PRO H 14 " ideal model delta sigma weight residual 112.00 103.09 8.91 1.40e+00 5.10e-01 4.05e+01 angle pdb=" N PRO H 14 " pdb=" CA PRO H 14 " pdb=" C PRO H 14 " ideal model delta sigma weight residual 110.55 118.61 -8.06 1.63e+00 3.76e-01 2.45e+01 angle pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 112.60 119.56 -6.96 1.70e+00 3.46e-01 1.68e+01 angle pdb=" CA LEU H 63 " pdb=" CB LEU H 63 " pdb=" CG LEU H 63 " ideal model delta sigma weight residual 116.30 126.99 -10.69 3.50e+00 8.16e-02 9.33e+00 ... (remaining 3461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.80: 1304 13.80 - 27.59: 143 27.59 - 41.39: 42 41.39 - 55.18: 7 55.18 - 68.98: 1 Dihedral angle restraints: 1497 sinusoidal: 590 harmonic: 907 Sorted by residual: dihedral pdb=" CA ASN C 487 " pdb=" C ASN C 487 " pdb=" N CYS C 488 " pdb=" CA CYS C 488 " ideal model delta harmonic sigma weight residual -180.00 -154.32 -25.68 0 5.00e+00 4.00e-02 2.64e+01 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 93.00 132.19 -39.19 1 1.00e+01 1.00e-02 2.16e+01 dihedral pdb=" CA VAL C 483 " pdb=" C VAL C 483 " pdb=" N GLU C 484 " pdb=" CA GLU C 484 " ideal model delta harmonic sigma weight residual 180.00 -158.37 -21.63 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 1494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 280 0.061 - 0.122: 77 0.122 - 0.183: 10 0.183 - 0.243: 2 0.243 - 0.304: 2 Chirality restraints: 371 Sorted by residual: chirality pdb=" CA PRO H 14 " pdb=" N PRO H 14 " pdb=" C PRO H 14 " pdb=" CB PRO H 14 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB THR C 470 " pdb=" CA THR C 470 " pdb=" OG1 THR C 470 " pdb=" CG2 THR C 470 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ASN C 440 " pdb=" N ASN C 440 " pdb=" C ASN C 440 " pdb=" CB ASN C 440 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 368 not shown) Planarity restraints: 448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " -0.058 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO H 14 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 473 " -0.013 2.00e-02 2.50e+03 1.86e-02 6.95e+00 pdb=" CG TYR C 473 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR C 473 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR C 473 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR C 473 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 473 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 473 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 473 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO C 521 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.032 5.00e-02 4.00e+02 ... (remaining 445 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 703 2.81 - 3.33: 1952 3.33 - 3.86: 3972 3.86 - 4.38: 4564 4.38 - 4.90: 8063 Nonbonded interactions: 19254 Sorted by model distance: nonbonded pdb=" OD1 ASN C 450 " pdb=" OG SER H 56 " model vdw 2.288 3.040 nonbonded pdb=" NE ARG C 457 " pdb=" OD2 ASP C 467 " model vdw 2.401 3.120 nonbonded pdb=" O4 NAG C1301 " pdb=" O6 NAG C1301 " model vdw 2.486 3.040 nonbonded pdb=" O ILE C 418 " pdb=" N TYR C 423 " model vdw 2.514 3.120 nonbonded pdb=" NH2 ARG C 454 " pdb=" O ASP C 467 " model vdw 2.528 3.120 ... (remaining 19249 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.460 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.770 Find NCS groups from input model: 0.010 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 0.121 2553 Z= 0.271 Angle : 1.011 11.238 3479 Z= 0.567 Chirality : 0.060 0.304 371 Planarity : 0.009 0.083 447 Dihedral : 12.719 68.980 910 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -1.78 (0.40), residues: 310 helix: -4.74 (0.24), residues: 26 sheet: -0.29 (0.50), residues: 96 loop : -1.12 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 19 TYR 0.046 0.002 TYR C 473 PHE 0.020 0.003 PHE C 497 TRP 0.016 0.002 TRP H 109 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00619 ( 2547) covalent geometry : angle 1.00581 ( 3466) SS BOND : bond 0.00310 ( 5) SS BOND : angle 1.72891 ( 10) hydrogen bonds : bond 0.13297 ( 73) hydrogen bonds : angle 9.34903 ( 183) link_NAG-ASN : bond 0.00526 ( 1) link_NAG-ASN : angle 2.40853 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: H 60 ASN cc_start: 0.9086 (t0) cc_final: 0.8884 (t0) REVERT: H 98 VAL cc_start: 0.8299 (m) cc_final: 0.8026 (t) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0740 time to fit residues: 6.8299 Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.116097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.099351 restraints weight = 4552.944| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.21 r_work: 0.3165 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2553 Z= 0.154 Angle : 0.608 9.165 3479 Z= 0.308 Chirality : 0.046 0.146 371 Planarity : 0.005 0.045 447 Dihedral : 5.718 25.708 372 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.12 % Allowed : 9.36 % Favored : 89.51 % 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: -1.40 (0.41), residues: 310 helix: -3.55 (0.65), residues: 26 sheet: -0.19 (0.50), residues: 96 loop : -0.90 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 466 TYR 0.010 0.001 TYR C 495 PHE 0.013 0.001 PHE C 377 TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 2547) covalent geometry : angle 0.60636 ( 3466) SS BOND : bond 0.00170 ( 5) SS BOND : angle 0.61054 ( 10) hydrogen bonds : bond 0.03276 ( 73) hydrogen bonds : angle 7.26618 ( 183) link_NAG-ASN : bond 0.00419 ( 1) link_NAG-ASN : angle 1.59219 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: C 417 LYS cc_start: 0.8372 (mmtp) cc_final: 0.7983 (mtpt) REVERT: H 13 GLN cc_start: 0.8384 (mp10) cc_final: 0.8172 (mp10) REVERT: H 19 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7573 (tpt-90) REVERT: H 60 ASN cc_start: 0.9244 (t0) cc_final: 0.8779 (t0) outliers start: 3 outliers final: 3 residues processed: 83 average time/residue: 0.0738 time to fit residues: 7.0378 Evaluate side-chains 79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 24 optimal weight: 0.0010 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100574 restraints weight = 4645.329| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.16 r_work: 0.3184 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2553 Z= 0.121 Angle : 0.567 7.201 3479 Z= 0.285 Chirality : 0.044 0.139 371 Planarity : 0.004 0.036 447 Dihedral : 4.966 20.125 372 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.87 % Allowed : 11.61 % Favored : 86.52 % 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: -1.19 (0.42), residues: 310 helix: -3.25 (0.77), residues: 27 sheet: -0.07 (0.50), residues: 96 loop : -0.76 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 466 TYR 0.011 0.001 TYR C 473 PHE 0.024 0.001 PHE C 456 TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 2547) covalent geometry : angle 0.56552 ( 3466) SS BOND : bond 0.00059 ( 5) SS BOND : angle 0.62597 ( 10) hydrogen bonds : bond 0.02996 ( 73) hydrogen bonds : angle 6.75126 ( 183) link_NAG-ASN : bond 0.00422 ( 1) link_NAG-ASN : angle 1.41853 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.094 Fit side-chains REVERT: C 417 LYS cc_start: 0.8444 (mmtp) cc_final: 0.8041 (mtpt) REVERT: C 442 ASP cc_start: 0.9160 (m-30) cc_final: 0.8733 (m-30) REVERT: H 13 GLN cc_start: 0.8467 (mp10) cc_final: 0.8244 (mp10) REVERT: H 19 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7657 (tpp80) REVERT: H 60 ASN cc_start: 0.9161 (t0) cc_final: 0.8744 (t0) outliers start: 5 outliers final: 3 residues processed: 81 average time/residue: 0.0786 time to fit residues: 7.2558 Evaluate side-chains 75 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097557 restraints weight = 4656.091| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.07 r_work: 0.3123 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2553 Z= 0.182 Angle : 0.601 5.828 3479 Z= 0.301 Chirality : 0.045 0.137 371 Planarity : 0.004 0.035 447 Dihedral : 5.049 19.238 372 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.00 % Allowed : 14.98 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.24 (0.42), residues: 310 helix: -3.10 (0.88), residues: 27 sheet: -0.12 (0.49), residues: 96 loop : -0.82 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 466 TYR 0.011 0.001 TYR C 495 PHE 0.011 0.001 PHE C 377 TRP 0.006 0.001 TRP C 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 2547) covalent geometry : angle 0.59979 ( 3466) SS BOND : bond 0.00132 ( 5) SS BOND : angle 0.59254 ( 10) hydrogen bonds : bond 0.03045 ( 73) hydrogen bonds : angle 6.66970 ( 183) link_NAG-ASN : bond 0.00269 ( 1) link_NAG-ASN : angle 1.41265 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.091 Fit side-chains REVERT: C 417 LYS cc_start: 0.8423 (mmtp) cc_final: 0.8020 (mtpt) REVERT: H 19 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7534 (tpp80) REVERT: H 60 ASN cc_start: 0.9174 (t0) cc_final: 0.8749 (t0) REVERT: H 66 LEU cc_start: 0.7927 (mt) cc_final: 0.7700 (mm) outliers start: 8 outliers final: 5 residues processed: 79 average time/residue: 0.0842 time to fit residues: 7.5474 Evaluate side-chains 80 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.0570 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.116114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099523 restraints weight = 4597.383| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.18 r_work: 0.3152 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2553 Z= 0.120 Angle : 0.560 6.664 3479 Z= 0.280 Chirality : 0.044 0.132 371 Planarity : 0.004 0.039 447 Dihedral : 4.598 17.102 372 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.62 % Allowed : 16.85 % Favored : 80.52 % 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: -1.17 (0.42), residues: 310 helix: -3.02 (0.87), residues: 27 sheet: -0.10 (0.50), residues: 91 loop : -0.74 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.012 0.001 TYR H 79 PHE 0.009 0.001 PHE C 377 TRP 0.010 0.001 TRP H 36 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 2547) covalent geometry : angle 0.55897 ( 3466) SS BOND : bond 0.00163 ( 5) SS BOND : angle 0.53309 ( 10) hydrogen bonds : bond 0.02888 ( 73) hydrogen bonds : angle 6.41638 ( 183) link_NAG-ASN : bond 0.00338 ( 1) link_NAG-ASN : angle 1.29159 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.060 Fit side-chains REVERT: C 417 LYS cc_start: 0.8489 (mmtp) cc_final: 0.8087 (mtpt) REVERT: H 19 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7415 (tpp80) REVERT: H 60 ASN cc_start: 0.9153 (t0) cc_final: 0.8772 (t0) REVERT: H 66 LEU cc_start: 0.7976 (mt) cc_final: 0.7729 (mm) REVERT: H 81 GLN cc_start: 0.8591 (tp40) cc_final: 0.7813 (tp40) outliers start: 7 outliers final: 6 residues processed: 75 average time/residue: 0.0835 time to fit residues: 7.0509 Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 15 optimal weight: 0.0770 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098825 restraints weight = 4661.390| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.22 r_work: 0.3142 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2553 Z= 0.134 Angle : 0.567 5.766 3479 Z= 0.282 Chirality : 0.044 0.131 371 Planarity : 0.004 0.035 447 Dihedral : 4.502 16.707 372 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.12 % Allowed : 16.10 % Favored : 79.78 % 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: -1.14 (0.43), residues: 310 helix: -3.15 (0.84), residues: 27 sheet: -0.01 (0.51), residues: 91 loop : -0.74 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.009 0.001 TYR C 495 PHE 0.009 0.001 PHE C 377 TRP 0.005 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 2547) covalent geometry : angle 0.56626 ( 3466) SS BOND : bond 0.00160 ( 5) SS BOND : angle 0.47063 ( 10) hydrogen bonds : bond 0.02945 ( 73) hydrogen bonds : angle 6.34659 ( 183) link_NAG-ASN : bond 0.00298 ( 1) link_NAG-ASN : angle 1.22784 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.073 Fit side-chains REVERT: C 417 LYS cc_start: 0.8450 (mmtp) cc_final: 0.8050 (mtpt) REVERT: H 19 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7541 (tpp80) REVERT: H 60 ASN cc_start: 0.9172 (t0) cc_final: 0.8796 (t0) outliers start: 11 outliers final: 6 residues processed: 78 average time/residue: 0.0799 time to fit residues: 7.0908 Evaluate side-chains 78 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097650 restraints weight = 4608.672| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.13 r_work: 0.3125 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2553 Z= 0.163 Angle : 0.585 6.373 3479 Z= 0.294 Chirality : 0.045 0.142 371 Planarity : 0.004 0.036 447 Dihedral : 4.601 17.162 372 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.62 % Allowed : 17.23 % Favored : 80.15 % 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: -1.11 (0.43), residues: 310 helix: -2.98 (0.90), residues: 26 sheet: 0.02 (0.52), residues: 91 loop : -0.76 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.012 0.001 TYR H 79 PHE 0.010 0.001 PHE C 377 TRP 0.005 0.001 TRP C 436 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 2547) covalent geometry : angle 0.58433 ( 3466) SS BOND : bond 0.00142 ( 5) SS BOND : angle 0.49971 ( 10) hydrogen bonds : bond 0.03035 ( 73) hydrogen bonds : angle 6.37899 ( 183) link_NAG-ASN : bond 0.00267 ( 1) link_NAG-ASN : angle 1.29201 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.090 Fit side-chains REVERT: C 417 LYS cc_start: 0.8501 (mmtp) cc_final: 0.8114 (mtpt) REVERT: C 462 LYS cc_start: 0.9175 (mtmt) cc_final: 0.8759 (mmtm) REVERT: H 19 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7774 (ttm-80) REVERT: H 60 ASN cc_start: 0.9195 (t0) cc_final: 0.8799 (t0) REVERT: H 66 LEU cc_start: 0.8562 (mm) cc_final: 0.8171 (mt) REVERT: H 81 GLN cc_start: 0.8575 (tp40) cc_final: 0.8036 (tp40) outliers start: 7 outliers final: 7 residues processed: 73 average time/residue: 0.0766 time to fit residues: 6.3992 Evaluate side-chains 78 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098726 restraints weight = 4636.175| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.15 r_work: 0.3142 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2553 Z= 0.139 Angle : 0.568 7.119 3479 Z= 0.286 Chirality : 0.044 0.128 371 Planarity : 0.004 0.034 447 Dihedral : 4.432 16.812 372 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.00 % Allowed : 17.23 % Favored : 79.78 % 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: -0.97 (0.44), residues: 310 helix: -2.88 (0.93), residues: 26 sheet: 0.14 (0.52), residues: 96 loop : -0.70 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.015 0.001 TYR H 32 PHE 0.011 0.001 PHE H 29 TRP 0.005 0.001 TRP H 47 HIS 0.001 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 2547) covalent geometry : angle 0.56763 ( 3466) SS BOND : bond 0.00176 ( 5) SS BOND : angle 0.48846 ( 10) hydrogen bonds : bond 0.02964 ( 73) hydrogen bonds : angle 6.27737 ( 183) link_NAG-ASN : bond 0.00289 ( 1) link_NAG-ASN : angle 1.25395 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.089 Fit side-chains REVERT: C 417 LYS cc_start: 0.8513 (mmtp) cc_final: 0.8121 (mtpt) REVERT: C 462 LYS cc_start: 0.9134 (mtmt) cc_final: 0.8749 (mmtm) REVERT: H 19 ARG cc_start: 0.8089 (ttm-80) cc_final: 0.7488 (tpp80) REVERT: H 60 ASN cc_start: 0.9176 (t0) cc_final: 0.8796 (t0) REVERT: H 81 GLN cc_start: 0.8596 (tp40) cc_final: 0.7794 (tp40) outliers start: 8 outliers final: 7 residues processed: 74 average time/residue: 0.0849 time to fit residues: 7.0753 Evaluate side-chains 77 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.113182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097152 restraints weight = 4632.264| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.07 r_work: 0.3123 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2553 Z= 0.179 Angle : 0.600 7.387 3479 Z= 0.301 Chirality : 0.045 0.131 371 Planarity : 0.004 0.034 447 Dihedral : 4.628 17.159 372 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.62 % Allowed : 18.35 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.44), residues: 310 helix: -2.86 (0.94), residues: 26 sheet: 0.22 (0.52), residues: 96 loop : -0.76 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 403 TYR 0.012 0.001 TYR H 32 PHE 0.014 0.001 PHE H 29 TRP 0.007 0.001 TRP H 47 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 2547) covalent geometry : angle 0.59904 ( 3466) SS BOND : bond 0.00178 ( 5) SS BOND : angle 0.43758 ( 10) hydrogen bonds : bond 0.03021 ( 73) hydrogen bonds : angle 6.33447 ( 183) link_NAG-ASN : bond 0.00241 ( 1) link_NAG-ASN : angle 1.33208 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.091 Fit side-chains REVERT: C 417 LYS cc_start: 0.8507 (mmtp) cc_final: 0.8141 (mtpt) REVERT: C 462 LYS cc_start: 0.9165 (mtmt) cc_final: 0.8767 (mmtm) REVERT: H 19 ARG cc_start: 0.8051 (ttm-80) cc_final: 0.7754 (ttm-80) REVERT: H 60 ASN cc_start: 0.9205 (t0) cc_final: 0.8807 (t0) REVERT: H 66 LEU cc_start: 0.8594 (mm) cc_final: 0.7906 (pp) REVERT: H 81 GLN cc_start: 0.8589 (tp40) cc_final: 0.8058 (tp40) outliers start: 7 outliers final: 7 residues processed: 72 average time/residue: 0.0842 time to fit residues: 6.9116 Evaluate side-chains 77 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 0.0030 chunk 21 optimal weight: 2.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.098918 restraints weight = 4665.841| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.10 r_work: 0.3163 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2553 Z= 0.135 Angle : 0.573 7.615 3479 Z= 0.287 Chirality : 0.044 0.135 371 Planarity : 0.004 0.034 447 Dihedral : 4.421 16.684 372 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.62 % Allowed : 18.35 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.44), residues: 310 helix: -2.86 (0.93), residues: 26 sheet: 0.46 (0.54), residues: 90 loop : -0.67 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 403 TYR 0.009 0.001 TYR H 32 PHE 0.012 0.001 PHE H 29 TRP 0.006 0.001 TRP H 47 HIS 0.001 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 2547) covalent geometry : angle 0.57253 ( 3466) SS BOND : bond 0.00163 ( 5) SS BOND : angle 0.43897 ( 10) hydrogen bonds : bond 0.02901 ( 73) hydrogen bonds : angle 6.19250 ( 183) link_NAG-ASN : bond 0.00296 ( 1) link_NAG-ASN : angle 1.24918 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.116 Fit side-chains REVERT: C 417 LYS cc_start: 0.8497 (mmtp) cc_final: 0.8130 (mtpt) REVERT: C 462 LYS cc_start: 0.9144 (mtmt) cc_final: 0.8741 (mmtm) REVERT: H 19 ARG cc_start: 0.8084 (ttm-80) cc_final: 0.7481 (tpp80) REVERT: H 60 ASN cc_start: 0.9174 (t0) cc_final: 0.8807 (t0) REVERT: H 66 LEU cc_start: 0.8556 (mm) cc_final: 0.7892 (pp) REVERT: H 81 GLN cc_start: 0.8584 (tp40) cc_final: 0.7789 (tp40) outliers start: 7 outliers final: 7 residues processed: 72 average time/residue: 0.0784 time to fit residues: 6.3699 Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098038 restraints weight = 4685.482| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.09 r_work: 0.3152 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2553 Z= 0.154 Angle : 0.572 6.488 3479 Z= 0.288 Chirality : 0.044 0.129 371 Planarity : 0.004 0.034 447 Dihedral : 4.485 16.683 372 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.62 % Allowed : 17.98 % Favored : 79.40 % 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: -0.80 (0.45), residues: 310 helix: -2.87 (0.93), residues: 26 sheet: 0.53 (0.55), residues: 90 loop : -0.70 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 403 TYR 0.011 0.001 TYR H 79 PHE 0.013 0.001 PHE H 29 TRP 0.007 0.001 TRP H 47 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 2547) covalent geometry : angle 0.57172 ( 3466) SS BOND : bond 0.00167 ( 5) SS BOND : angle 0.43507 ( 10) hydrogen bonds : bond 0.02961 ( 73) hydrogen bonds : angle 6.21060 ( 183) link_NAG-ASN : bond 0.00255 ( 1) link_NAG-ASN : angle 1.29827 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 883.62 seconds wall clock time: 15 minutes 50.88 seconds (950.88 seconds total)