Starting phenix.real_space_refine on Wed Jul 1 21:10:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dm0_27522/07_2026/8dm0_27522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm0_27522/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8dm0_27522/07_2026/8dm0_27522.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dm0_27522/07_2026/8dm0_27522.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dm0_27522/07_2026/8dm0_27522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm0_27522/07_2026/8dm0_27522.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dm0_27522/07_2026/8dm0_27522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm0_27522/07_2026/8dm0_27522.map" } 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-6108/lib/python3.11/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 chiralities: 1 Time building chain proxies: 0.57, per 1000 atoms: 0.23 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: 0.18 Conformation dependent library (CDL) restraints added in 88.5 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: 0.32 Time building geometry restraints manager: 0.26 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: 1287 13.80 - 27.59: 141 27.59 - 41.39: 40 41.39 - 55.18: 7 55.18 - 68.98: 1 Dihedral angle restraints: 1476 sinusoidal: 569 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 1473 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: 4.100 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.450 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 12.687 68.980 889 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/Z covalent geometry : bond 0.00619 / 0.27 ( 2547) covalent geometry : angle 1.00581 / 0.57 ( 3466) SS BOND : bond 0.00310 / 0.15 ( 5) SS BOND : angle 1.72891 / 1.00 ( 10) hydrogen bonds : bond 0.13297 / 6.75 ( 73) hydrogen bonds : angle 9.34903 / 6.53 ( 183) link_NAG-ASN : bond 0.00526 / 0.28 ( 1) link_NAG-ASN : angle 2.40853 / 1.30 ( 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 : 0.098 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: 0.0678 time to fit residues: 6.3053 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 : 0.092 ------------------------------------------------------------------------------- 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: 0.6980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.115848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.099066 restraints weight = 4554.367| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.22 r_work: 0.3162 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2553 Z= 0.160 Angle : 0.606 9.120 3479 Z= 0.309 Chirality : 0.046 0.147 371 Planarity : 0.005 0.045 447 Dihedral : 5.298 24.539 351 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.12 % Allowed : 9.74 % Favored : 89.14 % 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: -3.53 (0.65), residues: 26 sheet: -0.19 (0.50), residues: 96 loop : -0.91 (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/Z covalent geometry : bond 0.00367 / 0.16 ( 2547) covalent geometry : angle 0.60582 / 0.31 ( 3466) SS BOND : bond 0.00240 / 0.13 ( 5) SS BOND : angle 0.61218 / 0.33 ( 10) hydrogen bonds : bond 0.03263 / 1.97 ( 73) hydrogen bonds : angle 7.23745 / 4.95 ( 183) link_NAG-ASN : bond 0.00463 / 0.24 ( 1) link_NAG-ASN : angle 1.10451 / 0.61 ( 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 : 0.092 Fit side-chains revert: symmetry clash REVERT: C 417 LYS cc_start: 0.8378 (mmtp) cc_final: 0.7998 (mtpt) REVERT: H 13 GLN cc_start: 0.8394 (mp10) cc_final: 0.8177 (mp10) REVERT: H 19 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7576 (tpt-90) REVERT: H 60 ASN cc_start: 0.9245 (t0) cc_final: 0.8778 (t0) outliers start: 3 outliers final: 3 residues processed: 83 average time/residue: 0.0649 time to fit residues: 6.2787 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 : 0.087 ------------------------------------------------------------------------------- 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: 0.3980 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 24 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.115886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.099466 restraints weight = 4598.972| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.15 r_work: 0.3167 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2059 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= 0.132 Angle : 0.566 7.094 3479 Z= 0.286 Chirality : 0.044 0.139 371 Planarity : 0.004 0.036 447 Dihedral : 4.944 20.779 351 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.62 % Allowed : 10.11 % Favored : 87.27 % 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: -1.22 (0.42), residues: 310 helix: -3.17 (0.81), residues: 27 sheet: -0.08 (0.50), residues: 96 loop : -0.81 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 466 TYR 0.012 0.001 TYR C 473 PHE 0.024 0.002 PHE C 456 TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 2547) covalent geometry : angle 0.56560 / 0.29 ( 3466) SS BOND : bond 0.00143 / 0.09 ( 5) SS BOND : angle 0.61745 / 0.35 ( 10) hydrogen bonds : bond 0.03050 / 1.83 ( 73) hydrogen bonds : angle 6.74740 / 4.63 ( 183) link_NAG-ASN : bond 0.00351 / 0.18 ( 1) link_NAG-ASN : angle 0.93510 / 0.52 ( 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 88 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.071 Fit side-chains REVERT: C 417 LYS cc_start: 0.8496 (mmtp) cc_final: 0.8099 (mtpt) REVERT: C 442 ASP cc_start: 0.9173 (m-30) cc_final: 0.8740 (m-30) REVERT: H 19 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7627 (tpp80) REVERT: H 60 ASN cc_start: 0.9148 (t0) cc_final: 0.8742 (t0) outliers start: 7 outliers final: 5 residues processed: 84 average time/residue: 0.0569 time to fit residues: 5.4824 Evaluate side-chains 78 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.066 ------------------------------------------------------------------------------- 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=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: 2.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 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: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.093996 restraints weight = 4727.377| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.08 r_work: 0.3061 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 2553 Z= 0.289 Angle : 0.672 6.205 3479 Z= 0.342 Chirality : 0.047 0.144 371 Planarity : 0.004 0.037 447 Dihedral : 5.394 19.067 351 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.49 % Allowed : 11.99 % Favored : 83.52 % 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: -1.51 (0.41), residues: 310 helix: -3.18 (0.85), residues: 27 sheet: -0.32 (0.48), residues: 96 loop : -1.02 (0.38), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 71 TYR 0.014 0.001 TYR C 495 PHE 0.014 0.002 PHE C 377 TRP 0.007 0.002 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.29 ( 2547) covalent geometry : angle 0.67131 / 0.34 ( 3466) SS BOND : bond 0.00224 / 0.11 ( 5) SS BOND : angle 0.71384 / 0.38 ( 10) hydrogen bonds : bond 0.03387 / 2.02 ( 73) hydrogen bonds : angle 6.98904 / 4.75 ( 183) link_NAG-ASN : bond 0.00171 / 0.09 ( 1) link_NAG-ASN : angle 1.22035 / 0.65 ( 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 85 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.091 Fit side-chains REVERT: C 417 LYS cc_start: 0.8520 (mmtp) cc_final: 0.8055 (mtmt) REVERT: H 19 ARG cc_start: 0.8086 (ttm-80) cc_final: 0.7583 (tpp80) REVERT: H 60 ASN cc_start: 0.9220 (t0) cc_final: 0.8792 (t0) outliers start: 12 outliers final: 8 residues processed: 79 average time/residue: 0.0623 time to fit residues: 5.6602 Evaluate side-chains 80 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 427 ASP 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 66 LEU 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: 0.9980 chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.096321 restraints weight = 4585.061| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.03 r_work: 0.3112 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2589 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= 0.172 Angle : 0.597 7.440 3479 Z= 0.301 Chirality : 0.045 0.138 371 Planarity : 0.004 0.037 447 Dihedral : 5.058 19.127 351 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.37 % Allowed : 15.73 % Favored : 80.90 % 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: -1.38 (0.42), residues: 310 helix: -2.93 (0.94), residues: 26 sheet: -0.25 (0.49), residues: 96 loop : -0.95 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 408 TYR 0.011 0.001 TYR C 473 PHE 0.010 0.001 PHE H 29 TRP 0.006 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 2547) covalent geometry : angle 0.59661 / 0.30 ( 3466) SS BOND : bond 0.00179 / 0.11 ( 5) SS BOND : angle 0.58677 / 0.31 ( 10) hydrogen bonds : bond 0.03134 / 1.88 ( 73) hydrogen bonds : angle 6.72603 / 4.55 ( 183) link_NAG-ASN : bond 0.00252 / 0.13 ( 1) link_NAG-ASN : angle 0.96333 / 0.53 ( 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 81 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.098 Fit side-chains REVERT: C 417 LYS cc_start: 0.8484 (mmtp) cc_final: 0.8079 (mtpt) REVERT: H 19 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7647 (ttm-80) REVERT: H 60 ASN cc_start: 0.9184 (t0) cc_final: 0.8799 (t0) REVERT: H 66 LEU cc_start: 0.8065 (mt) cc_final: 0.7784 (mm) REVERT: H 81 GLN cc_start: 0.8613 (tp40) cc_final: 0.8091 (tp40) outliers start: 9 outliers final: 7 residues processed: 77 average time/residue: 0.0737 time to fit residues: 6.4097 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 486 PHE Chi-restraints excluded: chain C residue 488 CYS 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 18 LEU 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: 0.0370 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.0270 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3509 r_free = 0.3509 target = 0.114145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.098338 restraints weight = 4630.674| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.05 r_work: 0.3139 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2553 Z= 0.131 Angle : 0.574 5.900 3479 Z= 0.286 Chirality : 0.044 0.146 371 Planarity : 0.004 0.035 447 Dihedral : 4.703 18.027 351 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.00 % Allowed : 16.85 % 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: -1.09 (0.43), residues: 310 helix: -2.72 (1.19), residues: 20 sheet: -0.12 (0.50), residues: 96 loop : -0.79 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.009 0.001 TYR C 473 PHE 0.009 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/Z covalent geometry : bond 0.00310 / 0.13 ( 2547) covalent geometry : angle 0.57431 / 0.29 ( 3466) SS BOND : bond 0.00198 / 0.13 ( 5) SS BOND : angle 0.50965 / 0.26 ( 10) hydrogen bonds : bond 0.02976 / 1.80 ( 73) hydrogen bonds : angle 6.42374 / 4.36 ( 183) link_NAG-ASN : bond 0.00276 / 0.15 ( 1) link_NAG-ASN : angle 0.87944 / 0.50 ( 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 77 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.055 Fit side-chains REVERT: C 417 LYS cc_start: 0.8480 (mmtp) cc_final: 0.8067 (mtpt) REVERT: H 19 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7437 (tpp80) REVERT: H 60 ASN cc_start: 0.9179 (t0) cc_final: 0.8822 (t0) REVERT: H 81 GLN cc_start: 0.8655 (tp40) cc_final: 0.7895 (tp40) outliers start: 8 outliers final: 7 residues processed: 72 average time/residue: 0.0673 time to fit residues: 5.4974 Evaluate side-chains 75 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU 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: 0.3980 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 13 optimal weight: 0.0050 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3525 r_free = 0.3525 target = 0.115103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.099006 restraints weight = 4601.625| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.06 r_work: 0.3155 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2873 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= 0.122 Angle : 0.567 6.596 3479 Z= 0.282 Chirality : 0.044 0.131 371 Planarity : 0.004 0.035 447 Dihedral : 4.479 17.010 351 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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: -1.06 (0.44), residues: 310 helix: -2.85 (0.94), residues: 26 sheet: -0.04 (0.50), residues: 96 loop : -0.70 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.011 0.001 TYR H 79 PHE 0.008 0.001 PHE C 377 TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 2547) covalent geometry : angle 0.56647 / 0.28 ( 3466) SS BOND : bond 0.00186 / 0.12 ( 5) SS BOND : angle 0.47163 / 0.24 ( 10) hydrogen bonds : bond 0.02933 / 1.76 ( 73) hydrogen bonds : angle 6.29853 / 4.28 ( 183) link_NAG-ASN : bond 0.00257 / 0.14 ( 1) link_NAG-ASN : angle 0.89209 / 0.50 ( 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 77 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.078 Fit side-chains REVERT: C 417 LYS cc_start: 0.8523 (mmtp) cc_final: 0.8108 (mtpt) REVERT: C 462 LYS cc_start: 0.9138 (mtmt) cc_final: 0.8735 (mmtm) REVERT: H 19 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7570 (tpp80) REVERT: H 60 ASN cc_start: 0.9180 (t0) cc_final: 0.8823 (t0) REVERT: H 66 LEU cc_start: 0.8551 (mm) cc_final: 0.8204 (mt) REVERT: H 81 GLN cc_start: 0.8642 (tp40) cc_final: 0.7934 (tp40) outliers start: 7 outliers final: 7 residues processed: 72 average time/residue: 0.0602 time to fit residues: 4.9332 Evaluate side-chains 75 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 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 18 LEU 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: 0.8980 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096925 restraints weight = 4672.915| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.10 r_work: 0.3114 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2553 Z= 0.182 Angle : 0.605 6.945 3479 Z= 0.303 Chirality : 0.045 0.140 371 Planarity : 0.004 0.035 447 Dihedral : 4.632 17.404 351 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.37 % Allowed : 17.98 % Favored : 78.65 % 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: -1.06 (0.44), residues: 310 helix: -2.88 (0.95), residues: 26 sheet: -0.04 (0.51), residues: 96 loop : -0.70 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.014 0.001 TYR C 473 PHE 0.014 0.001 PHE H 29 TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 2547) covalent geometry : angle 0.60411 / 0.30 ( 3466) SS BOND : bond 0.00219 / 0.11 ( 5) SS BOND : angle 0.65568 / 0.36 ( 10) hydrogen bonds : bond 0.03118 / 1.85 ( 73) hydrogen bonds : angle 6.33944 / 4.28 ( 183) link_NAG-ASN : bond 0.00178 / 0.09 ( 1) link_NAG-ASN : angle 1.04528 / 0.58 ( 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 77 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.092 Fit side-chains REVERT: C 417 LYS cc_start: 0.8494 (mmtp) cc_final: 0.8108 (mtpt) REVERT: C 462 LYS cc_start: 0.9179 (mtmt) cc_final: 0.8746 (mmtm) REVERT: H 3 GLN cc_start: 0.8279 (tp40) cc_final: 0.7880 (tm-30) REVERT: H 19 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7566 (tpp80) REVERT: H 32 TYR cc_start: 0.8157 (m-10) cc_final: 0.7762 (m-10) REVERT: H 60 ASN cc_start: 0.9205 (t0) cc_final: 0.8816 (t0) REVERT: H 81 GLN cc_start: 0.8648 (tp40) cc_final: 0.8427 (tp-100) outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 0.0797 time to fit residues: 6.4901 Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.055 ------------------------------------------------------------------------------- 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 18 LEU 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: 3.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.097006 restraints weight = 4637.310| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.03 r_work: 0.3122 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2553 Z= 0.172 Angle : 0.600 6.301 3479 Z= 0.301 Chirality : 0.045 0.137 371 Planarity : 0.004 0.035 447 Dihedral : 4.651 17.404 351 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.00 % Allowed : 17.60 % 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: -0.99 (0.44), residues: 310 helix: -2.85 (0.96), residues: 26 sheet: 0.13 (0.52), residues: 96 loop : -0.72 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 97 TYR 0.012 0.001 TYR C 473 PHE 0.013 0.001 PHE H 29 TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 2547) covalent geometry : angle 0.59981 / 0.30 ( 3466) SS BOND : bond 0.00209 / 0.11 ( 5) SS BOND : angle 0.63578 / 0.35 ( 10) hydrogen bonds : bond 0.03076 / 1.81 ( 73) hydrogen bonds : angle 6.34948 / 4.28 ( 183) link_NAG-ASN : bond 0.00198 / 0.10 ( 1) link_NAG-ASN : angle 0.98689 / 0.55 ( 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 75 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.055 Fit side-chains REVERT: C 417 LYS cc_start: 0.8487 (mmtp) cc_final: 0.8107 (mtpt) REVERT: C 462 LYS cc_start: 0.9168 (mtmt) cc_final: 0.8758 (mmtm) REVERT: H 3 GLN cc_start: 0.8295 (tp40) cc_final: 0.7893 (tm-30) REVERT: H 19 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7504 (tpp80) REVERT: H 60 ASN cc_start: 0.9201 (t0) cc_final: 0.8821 (t0) REVERT: H 66 LEU cc_start: 0.8612 (mm) cc_final: 0.7910 (pp) REVERT: H 81 GLN cc_start: 0.8648 (tp40) cc_final: 0.8418 (tp-100) outliers start: 8 outliers final: 8 residues processed: 70 average time/residue: 0.0622 time to fit residues: 4.9667 Evaluate side-chains 75 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 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 18 LEU 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: 0.6980 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.0470 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 0.0270 chunk 21 optimal weight: 0.7980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3536 r_free = 0.3536 target = 0.115596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099550 restraints weight = 4650.313| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.12 r_work: 0.3156 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2553 Z= 0.121 Angle : 0.573 5.723 3479 Z= 0.286 Chirality : 0.044 0.132 371 Planarity : 0.004 0.036 447 Dihedral : 4.423 17.594 351 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.00 % Allowed : 17.98 % 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: -0.86 (0.45), residues: 310 helix: -2.82 (0.97), residues: 26 sheet: 0.31 (0.54), residues: 90 loop : -0.66 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 97 TYR 0.010 0.001 TYR C 473 PHE 0.010 0.001 PHE H 29 TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 2547) covalent geometry : angle 0.57311 / 0.29 ( 3466) SS BOND : bond 0.00196 / 0.11 ( 5) SS BOND : angle 0.56251 / 0.31 ( 10) hydrogen bonds : bond 0.02931 / 1.76 ( 73) hydrogen bonds : angle 6.20774 / 4.20 ( 183) link_NAG-ASN : bond 0.00242 / 0.13 ( 1) link_NAG-ASN : angle 0.88321 / 0.50 ( 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 75 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.091 Fit side-chains REVERT: C 417 LYS cc_start: 0.8500 (mmtp) cc_final: 0.8099 (mtpt) REVERT: C 462 LYS cc_start: 0.9132 (mtmt) cc_final: 0.8725 (mmtm) REVERT: H 3 GLN cc_start: 0.8285 (tp40) cc_final: 0.7880 (tm-30) REVERT: H 19 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7612 (tpp80) REVERT: H 60 ASN cc_start: 0.9181 (t0) cc_final: 0.8824 (t0) REVERT: H 66 LEU cc_start: 0.8566 (mm) cc_final: 0.7889 (pp) REVERT: H 81 GLN cc_start: 0.8624 (tp40) cc_final: 0.8421 (tp-100) outliers start: 8 outliers final: 8 residues processed: 70 average time/residue: 0.0646 time to fit residues: 5.1503 Evaluate side-chains 74 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.096 ------------------------------------------------------------------------------- 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 18 LEU 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: 0.8980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 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... ** 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 = 0.113561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097476 restraints weight = 4693.386| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.15 r_work: 0.3125 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3001 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= 0.157 Angle : 0.592 6.254 3479 Z= 0.297 Chirality : 0.045 0.134 371 Planarity : 0.004 0.035 447 Dihedral : 4.495 16.962 351 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.37 % Allowed : 17.60 % 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: -0.87 (0.45), residues: 310 helix: -2.87 (0.94), residues: 26 sheet: 0.36 (0.54), residues: 90 loop : -0.68 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 97 TYR 0.011 0.001 TYR C 473 PHE 0.012 0.001 PHE H 29 TRP 0.009 0.001 TRP H 47 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 2547) covalent geometry : angle 0.59195 / 0.30 ( 3466) SS BOND : bond 0.00187 / 0.10 ( 5) SS BOND : angle 0.60005 / 0.33 ( 10) hydrogen bonds : bond 0.03047 / 1.81 ( 73) hydrogen bonds : angle 6.23541 / 4.21 ( 183) link_NAG-ASN : bond 0.00207 / 0.11 ( 1) link_NAG-ASN : angle 0.96916 / 0.54 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 764.60 seconds wall clock time: 13 minutes 48.97 seconds (828.97 seconds total)