Starting phenix.real_space_refine on Tue Mar 3 11:30:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tly_25990/03_2026/7tly_25990.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tly_25990/03_2026/7tly_25990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tly_25990/03_2026/7tly_25990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tly_25990/03_2026/7tly_25990.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tly_25990/03_2026/7tly_25990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tly_25990/03_2026/7tly_25990.map" } resolution = 3.0 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= 0.034 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 1990 2.51 5 N 534 2.21 5 O 568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 3105 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 950 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 718 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1388 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 11, 'TRANS': 169} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 5, 'PHE:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 0.83, per 1000 atoms: 0.27 Number of scatterers: 3105 At special positions: 0 Unit cell: (69.969, 74.184, 79.242, 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 568 8.00 N 534 7.00 C 1990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS I 336 " - pdb=" SG CYS I 361 " distance=2.03 Simple disulfide: pdb=" SG CYS I 379 " - pdb=" SG CYS I 432 " distance=2.04 Simple disulfide: pdb=" SG CYS I 391 " - pdb=" SG CYS I 525 " distance=2.10 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " NAG C 1 " - " FUC C 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN I 343 " Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 130.0 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 9 sheets defined 13.5% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.580A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'I' and resid 338 through 343 Processing helix chain 'I' and resid 349 through 353 removed outlier: 3.747A pdb=" N TRP I 353 " --> pdb=" O VAL I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 371 Processing helix chain 'I' and resid 386 through 389 Processing helix chain 'I' and resid 405 through 410 removed outlier: 4.432A pdb=" N ARG I 408 " --> pdb=" O ASP I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 443 Processing helix chain 'I' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.857A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.735A pdb=" N ASN A 116 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 11 removed outlier: 7.040A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 Processing sheet with id=AA7, first strand: chain 'I' and resid 354 through 358 removed outlier: 3.666A pdb=" N ASN I 394 " --> pdb=" O GLU I 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 361 through 362 removed outlier: 6.503A pdb=" N CYS I 361 " --> pdb=" O CYS I 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 452 through 454 126 hydrogen bonds defined for protein. 282 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: 0.41 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 709 1.33 - 1.45: 786 1.45 - 1.58: 1672 1.58 - 1.70: 2 1.70 - 1.83: 16 Bond restraints: 3185 Sorted by residual: bond pdb=" N ASN I 388 " pdb=" CA ASN I 388 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.21e+00 bond pdb=" CB ILE I 332 " pdb=" CG1 ILE I 332 " ideal model delta sigma weight residual 1.530 1.588 -0.058 2.00e-02 2.50e+03 8.41e+00 bond pdb=" N ASN I 417 " pdb=" CA ASN I 417 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.35e-02 5.49e+03 7.56e+00 bond pdb=" N PRO B 8 " pdb=" CD PRO B 8 " ideal model delta sigma weight residual 1.474 1.512 -0.038 1.40e-02 5.10e+03 7.56e+00 bond pdb=" NE ARG I 457 " pdb=" CZ ARG I 457 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.55e+00 ... (remaining 3180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 4056 2.31 - 4.62: 217 4.62 - 6.93: 52 6.93 - 9.24: 7 9.24 - 11.55: 4 Bond angle restraints: 4336 Sorted by residual: angle pdb=" N ASP I 389 " pdb=" CA ASP I 389 " pdb=" C ASP I 389 " ideal model delta sigma weight residual 112.92 123.82 -10.90 1.23e+00 6.61e-01 7.85e+01 angle pdb=" N ASP I 389 " pdb=" CA ASP I 389 " pdb=" CB ASP I 389 " ideal model delta sigma weight residual 110.56 99.78 10.78 1.46e+00 4.69e-01 5.45e+01 angle pdb=" C ILE B 59 " pdb=" N PRO B 60 " pdb=" CA PRO B 60 " ideal model delta sigma weight residual 119.78 127.10 -7.32 1.03e+00 9.43e-01 5.06e+01 angle pdb=" C ARG I 498 " pdb=" N PRO I 499 " pdb=" CA PRO I 499 " ideal model delta sigma weight residual 119.87 127.21 -7.34 1.04e+00 9.25e-01 4.98e+01 angle pdb=" C PHE I 490 " pdb=" N PRO I 491 " pdb=" CA PRO I 491 " ideal model delta sigma weight residual 119.56 126.56 -7.00 1.02e+00 9.61e-01 4.71e+01 ... (remaining 4331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.31: 1824 21.31 - 42.61: 52 42.61 - 63.92: 8 63.92 - 85.22: 8 85.22 - 106.53: 5 Dihedral angle restraints: 1897 sinusoidal: 724 harmonic: 1173 Sorted by residual: dihedral pdb=" C ALA B 52 " pdb=" N ALA B 52 " pdb=" CA ALA B 52 " pdb=" CB ALA B 52 " ideal model delta harmonic sigma weight residual -122.60 -136.01 13.41 0 2.50e+00 1.60e-01 2.88e+01 dihedral pdb=" N SER B 53 " pdb=" C SER B 53 " pdb=" CA SER B 53 " pdb=" CB SER B 53 " ideal model delta harmonic sigma weight residual 122.80 112.34 10.46 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 60.32 32.68 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 1894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 383 0.096 - 0.192: 80 0.192 - 0.288: 12 0.288 - 0.384: 3 0.384 - 0.480: 1 Chirality restraints: 479 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.53e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.06e+01 chirality pdb=" CA ALA B 52 " pdb=" N ALA B 52 " pdb=" C ALA B 52 " pdb=" CB ALA B 52 " both_signs ideal model delta sigma weight residual False 2.48 2.01 0.48 2.00e-01 2.50e+01 5.75e+00 ... (remaining 476 not shown) Planarity restraints: 554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 461 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C LEU I 461 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU I 461 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS I 462 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 31 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C SER B 31 " 0.031 2.00e-02 2.50e+03 pdb=" O SER B 31 " -0.012 2.00e-02 2.50e+03 pdb=" N THR B 32 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 495 " -0.023 2.00e-02 2.50e+03 1.20e-02 2.87e+00 pdb=" CG TYR I 495 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR I 495 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR I 495 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR I 495 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR I 495 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR I 495 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR I 495 " -0.017 2.00e-02 2.50e+03 ... (remaining 551 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.02: 1742 3.02 - 3.49: 2674 3.49 - 3.96: 5157 3.96 - 4.43: 5922 4.43 - 4.90: 9437 Nonbonded interactions: 24932 Sorted by model distance: nonbonded pdb=" O GLN B 6 " pdb=" OG SER B 7 " model vdw 2.556 3.040 nonbonded pdb=" OD1 ASP A 115 " pdb=" N ASN A 116 " model vdw 2.586 3.120 nonbonded pdb=" N ASP I 428 " pdb=" OD1 ASP I 428 " model vdw 2.591 3.120 nonbonded pdb=" N LEU I 387 " pdb=" N ASN I 388 " model vdw 2.592 2.560 nonbonded pdb=" N LYS I 462 " pdb=" O LYS I 462 " model vdw 2.611 2.496 ... (remaining 24927 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: 15.920 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: 0.080 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.090 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 : 0.010 0.074 3194 Z= 0.576 Angle : 1.328 11.553 4358 Z= 0.895 Chirality : 0.083 0.480 479 Planarity : 0.005 0.025 553 Dihedral : 12.976 106.526 1138 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 5.56 % 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: 0.36 (0.41), residues: 396 helix: -3.25 (0.69), residues: 33 sheet: 0.71 (0.40), residues: 157 loop : 0.65 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 493 TYR 0.023 0.003 TYR I 495 PHE 0.013 0.003 PHE B 98 TRP 0.018 0.004 TRP A 50 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00998 ( 3185) covalent geometry : angle 1.32024 ( 4336) SS BOND : bond 0.03371 ( 5) SS BOND : angle 2.51708 ( 10) hydrogen bonds : bond 0.17018 ( 116) hydrogen bonds : angle 8.84395 ( 282) link_BETA1-4 : bond 0.05749 ( 2) link_BETA1-4 : angle 2.55125 ( 6) link_BETA1-6 : bond 0.04853 ( 1) link_BETA1-6 : angle 1.46037 ( 3) link_NAG-ASN : bond 0.05745 ( 1) link_NAG-ASN : angle 2.44605 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 90 ASP cc_start: 0.5815 (m-30) cc_final: 0.5444 (m-30) REVERT: A 95 TYR cc_start: 0.7806 (m-80) cc_final: 0.7444 (m-80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.5327 time to fit residues: 35.0273 Evaluate side-chains 42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.164576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.153178 restraints weight = 4175.094| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.39 r_work: 0.3575 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3194 Z= 0.181 Angle : 0.649 9.618 4358 Z= 0.332 Chirality : 0.049 0.166 479 Planarity : 0.006 0.054 553 Dihedral : 8.017 56.586 531 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.51 % Allowed : 9.12 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.04 (0.40), residues: 396 helix: -2.49 (1.01), residues: 26 sheet: 0.64 (0.40), residues: 152 loop : -0.11 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 84 TYR 0.015 0.002 TYR A 94 PHE 0.015 0.002 PHE I 429 TRP 0.013 0.002 TRP A 117 HIS 0.004 0.002 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 3185) covalent geometry : angle 0.63948 ( 4336) SS BOND : bond 0.00273 ( 5) SS BOND : angle 1.12671 ( 10) hydrogen bonds : bond 0.04506 ( 116) hydrogen bonds : angle 6.62970 ( 282) link_BETA1-4 : bond 0.00434 ( 2) link_BETA1-4 : angle 2.46710 ( 6) link_BETA1-6 : bond 0.00782 ( 1) link_BETA1-6 : angle 1.51515 ( 3) link_NAG-ASN : bond 0.00673 ( 1) link_NAG-ASN : angle 1.56756 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7043 (mm-40) outliers start: 10 outliers final: 3 residues processed: 56 average time/residue: 0.6175 time to fit residues: 35.5377 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 13 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.158932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.149049 restraints weight = 4125.793| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.15 r_work: 0.3516 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3194 Z= 0.254 Angle : 0.724 11.180 4358 Z= 0.364 Chirality : 0.051 0.157 479 Planarity : 0.006 0.056 553 Dihedral : 5.846 37.430 531 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.16 % Allowed : 12.28 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.84 (0.39), residues: 396 helix: -3.13 (0.78), residues: 32 sheet: 0.30 (0.41), residues: 141 loop : -0.69 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 24 TYR 0.022 0.002 TYR A 95 PHE 0.017 0.002 PHE I 429 TRP 0.015 0.002 TRP A 50 HIS 0.004 0.002 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 3185) covalent geometry : angle 0.71637 ( 4336) SS BOND : bond 0.00372 ( 5) SS BOND : angle 1.28712 ( 10) hydrogen bonds : bond 0.05223 ( 116) hydrogen bonds : angle 6.54004 ( 282) link_BETA1-4 : bond 0.00635 ( 2) link_BETA1-4 : angle 2.27865 ( 6) link_BETA1-6 : bond 0.00052 ( 1) link_BETA1-6 : angle 1.51322 ( 3) link_NAG-ASN : bond 0.00654 ( 1) link_NAG-ASN : angle 1.07493 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.115 Fit side-chains REVERT: A 59 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.7964 (t0) REVERT: A 119 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.6691 (pm20) REVERT: I 457 ARG cc_start: 0.8146 (ttt90) cc_final: 0.7813 (ttt90) outliers start: 9 outliers final: 4 residues processed: 46 average time/residue: 0.6352 time to fit residues: 29.9581 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.157610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.148013 restraints weight = 4102.913| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.13 r_work: 0.3512 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3194 Z= 0.224 Angle : 0.660 12.586 4358 Z= 0.327 Chirality : 0.048 0.145 479 Planarity : 0.006 0.059 553 Dihedral : 5.051 25.480 531 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.16 % Allowed : 12.63 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.39), residues: 396 helix: -3.28 (0.73), residues: 33 sheet: 0.24 (0.42), residues: 143 loop : -0.97 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 62 TYR 0.017 0.002 TYR A 95 PHE 0.011 0.002 PHE I 429 TRP 0.012 0.002 TRP A 50 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 3185) covalent geometry : angle 0.65194 ( 4336) SS BOND : bond 0.00316 ( 5) SS BOND : angle 1.12664 ( 10) hydrogen bonds : bond 0.04585 ( 116) hydrogen bonds : angle 6.43153 ( 282) link_BETA1-4 : bond 0.00484 ( 2) link_BETA1-4 : angle 2.23283 ( 6) link_BETA1-6 : bond 0.00034 ( 1) link_BETA1-6 : angle 1.53326 ( 3) link_NAG-ASN : bond 0.00436 ( 1) link_NAG-ASN : angle 1.21514 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.115 Fit side-chains REVERT: A 119 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.6706 (pm20) REVERT: I 346 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7717 (ttm-80) REVERT: I 457 ARG cc_start: 0.8165 (ttt90) cc_final: 0.7769 (ttt90) REVERT: I 465 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7707 (tt0) outliers start: 9 outliers final: 5 residues processed: 48 average time/residue: 0.6145 time to fit residues: 30.2382 Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 465 GLU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 25 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.159248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.149762 restraints weight = 4104.279| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.12 r_work: 0.3526 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3194 Z= 0.160 Angle : 0.585 11.251 4358 Z= 0.291 Chirality : 0.045 0.139 479 Planarity : 0.006 0.057 553 Dihedral : 4.505 17.956 531 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.81 % Allowed : 13.33 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.07 (0.39), residues: 396 helix: -3.32 (0.74), residues: 32 sheet: 0.30 (0.43), residues: 141 loop : -0.96 (0.37), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.016 0.001 TYR A 95 PHE 0.007 0.001 PHE B 63 TRP 0.007 0.001 TRP A 50 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 3185) covalent geometry : angle 0.57858 ( 4336) SS BOND : bond 0.00278 ( 5) SS BOND : angle 0.91576 ( 10) hydrogen bonds : bond 0.04007 ( 116) hydrogen bonds : angle 6.21202 ( 282) link_BETA1-4 : bond 0.00415 ( 2) link_BETA1-4 : angle 1.95416 ( 6) link_BETA1-6 : bond 0.00087 ( 1) link_BETA1-6 : angle 1.40869 ( 3) link_NAG-ASN : bond 0.00359 ( 1) link_NAG-ASN : angle 1.25945 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.121 Fit side-chains REVERT: I 346 ARG cc_start: 0.7936 (ttm-80) cc_final: 0.7588 (mtm-85) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.5558 time to fit residues: 29.1045 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.156253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.146688 restraints weight = 4124.007| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.13 r_work: 0.3486 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3194 Z= 0.258 Angle : 0.693 12.002 4358 Z= 0.347 Chirality : 0.049 0.153 479 Planarity : 0.007 0.057 553 Dihedral : 4.959 19.126 531 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.21 % Allowed : 13.68 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.45 (0.39), residues: 396 helix: -3.37 (0.71), residues: 33 sheet: 0.06 (0.42), residues: 143 loop : -1.27 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 62 TYR 0.020 0.002 TYR A 95 PHE 0.011 0.002 PHE I 392 TRP 0.012 0.002 TRP A 50 HIS 0.004 0.002 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00611 ( 3185) covalent geometry : angle 0.68667 ( 4336) SS BOND : bond 0.00390 ( 5) SS BOND : angle 1.23597 ( 10) hydrogen bonds : bond 0.04842 ( 116) hydrogen bonds : angle 6.59036 ( 282) link_BETA1-4 : bond 0.00442 ( 2) link_BETA1-4 : angle 1.94787 ( 6) link_BETA1-6 : bond 0.00132 ( 1) link_BETA1-6 : angle 1.59175 ( 3) link_NAG-ASN : bond 0.00326 ( 1) link_NAG-ASN : angle 1.07200 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.115 Fit side-chains REVERT: A 119 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.6814 (pm20) REVERT: I 346 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7665 (mtm-85) REVERT: I 465 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7744 (tt0) outliers start: 12 outliers final: 8 residues processed: 47 average time/residue: 0.6436 time to fit residues: 31.0406 Evaluate side-chains 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 465 GLU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 13 optimal weight: 0.2980 chunk 23 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.157970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.148512 restraints weight = 4140.573| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.12 r_work: 0.3506 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3194 Z= 0.172 Angle : 0.588 10.874 4358 Z= 0.294 Chirality : 0.046 0.139 479 Planarity : 0.006 0.055 553 Dihedral : 4.452 18.409 531 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.81 % Allowed : 15.44 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.45 (0.39), residues: 396 helix: -3.49 (0.69), residues: 33 sheet: 0.07 (0.43), residues: 144 loop : -1.26 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 62 TYR 0.018 0.001 TYR A 95 PHE 0.007 0.001 PHE I 429 TRP 0.010 0.002 TRP A 50 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3185) covalent geometry : angle 0.58093 ( 4336) SS BOND : bond 0.00295 ( 5) SS BOND : angle 0.93993 ( 10) hydrogen bonds : bond 0.04013 ( 116) hydrogen bonds : angle 6.29824 ( 282) link_BETA1-4 : bond 0.00439 ( 2) link_BETA1-4 : angle 1.91441 ( 6) link_BETA1-6 : bond 0.00049 ( 1) link_BETA1-6 : angle 1.44036 ( 3) link_NAG-ASN : bond 0.00254 ( 1) link_NAG-ASN : angle 1.31695 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.129 Fit side-chains REVERT: I 346 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7707 (mtm-85) REVERT: I 465 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7719 (tt0) outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.6457 time to fit residues: 27.8463 Evaluate side-chains 44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 465 GLU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.0040 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 35 optimal weight: 0.0870 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 overall best weight: 0.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.157763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.148257 restraints weight = 4250.769| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.14 r_work: 0.3510 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3194 Z= 0.177 Angle : 0.593 10.504 4358 Z= 0.298 Chirality : 0.046 0.144 479 Planarity : 0.006 0.054 553 Dihedral : 4.451 18.525 531 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.86 % Allowed : 14.74 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.41 (0.39), residues: 396 helix: -3.55 (0.67), residues: 33 sheet: 0.11 (0.43), residues: 144 loop : -1.23 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 62 TYR 0.018 0.001 TYR A 95 PHE 0.010 0.001 PHE I 392 TRP 0.008 0.002 TRP A 117 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 3185) covalent geometry : angle 0.58716 ( 4336) SS BOND : bond 0.00326 ( 5) SS BOND : angle 0.96602 ( 10) hydrogen bonds : bond 0.04059 ( 116) hydrogen bonds : angle 6.28785 ( 282) link_BETA1-4 : bond 0.00410 ( 2) link_BETA1-4 : angle 1.78860 ( 6) link_BETA1-6 : bond 0.00081 ( 1) link_BETA1-6 : angle 1.48266 ( 3) link_NAG-ASN : bond 0.00256 ( 1) link_NAG-ASN : angle 1.15755 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.120 Fit side-chains REVERT: A 90 ASP cc_start: 0.6784 (m-30) cc_final: 0.6189 (m-30) REVERT: A 119 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.6968 (pm20) REVERT: B 24 ARG cc_start: 0.8009 (tpp80) cc_final: 0.7745 (tpp80) REVERT: I 346 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7642 (mtm-85) REVERT: I 465 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7724 (tt0) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.6105 time to fit residues: 28.1728 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 465 GLU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 29 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.159283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.149918 restraints weight = 4167.175| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.11 r_work: 0.3527 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3194 Z= 0.132 Angle : 0.547 9.118 4358 Z= 0.274 Chirality : 0.044 0.133 479 Planarity : 0.006 0.055 553 Dihedral : 4.208 18.082 531 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.51 % Allowed : 15.09 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.30 (0.39), residues: 396 helix: -3.56 (0.67), residues: 33 sheet: 0.27 (0.44), residues: 142 loop : -1.20 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 62 TYR 0.017 0.001 TYR A 95 PHE 0.006 0.001 PHE B 84 TRP 0.006 0.001 TRP A 117 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3185) covalent geometry : angle 0.54095 ( 4336) SS BOND : bond 0.00245 ( 5) SS BOND : angle 0.79919 ( 10) hydrogen bonds : bond 0.03591 ( 116) hydrogen bonds : angle 6.10284 ( 282) link_BETA1-4 : bond 0.00423 ( 2) link_BETA1-4 : angle 1.70467 ( 6) link_BETA1-6 : bond 0.00114 ( 1) link_BETA1-6 : angle 1.35210 ( 3) link_NAG-ASN : bond 0.00231 ( 1) link_NAG-ASN : angle 1.29074 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.112 Fit side-chains REVERT: A 90 ASP cc_start: 0.6856 (m-30) cc_final: 0.6235 (m-30) REVERT: A 119 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7002 (pm20) REVERT: B 24 ARG cc_start: 0.7960 (tpp80) cc_final: 0.7706 (tpp80) REVERT: B 96 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8522 (tt) REVERT: I 346 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7640 (mtm-85) outliers start: 10 outliers final: 6 residues processed: 47 average time/residue: 0.6172 time to fit residues: 29.7745 Evaluate side-chains 45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 441 LEU Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 0.3980 chunk 36 optimal weight: 0.0980 chunk 31 optimal weight: 0.0030 chunk 15 optimal weight: 0.0870 chunk 19 optimal weight: 0.0170 chunk 37 optimal weight: 0.2980 chunk 38 optimal weight: 0.0370 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 overall best weight: 0.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.163337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.153716 restraints weight = 4075.809| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.16 r_work: 0.3565 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3194 Z= 0.078 Angle : 0.461 5.592 4358 Z= 0.235 Chirality : 0.042 0.132 479 Planarity : 0.005 0.051 553 Dihedral : 3.755 18.083 531 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.75 % Allowed : 16.49 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.91 (0.40), residues: 396 helix: -3.20 (0.82), residues: 26 sheet: 0.48 (0.44), residues: 141 loop : -1.00 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 62 TYR 0.016 0.001 TYR A 95 PHE 0.005 0.001 PHE B 84 TRP 0.008 0.001 TRP I 436 HIS 0.000 0.000 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00169 ( 3185) covalent geometry : angle 0.45446 ( 4336) SS BOND : bond 0.00208 ( 5) SS BOND : angle 0.64296 ( 10) hydrogen bonds : bond 0.02859 ( 116) hydrogen bonds : angle 5.60995 ( 282) link_BETA1-4 : bond 0.00438 ( 2) link_BETA1-4 : angle 1.54748 ( 6) link_BETA1-6 : bond 0.00401 ( 1) link_BETA1-6 : angle 1.23569 ( 3) link_NAG-ASN : bond 0.00214 ( 1) link_NAG-ASN : angle 1.42138 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.121 Fit side-chains REVERT: A 32 TYR cc_start: 0.8543 (m-80) cc_final: 0.8300 (m-80) REVERT: A 90 ASP cc_start: 0.6803 (m-30) cc_final: 0.6236 (m-30) REVERT: B 24 ARG cc_start: 0.7869 (tpp80) cc_final: 0.7629 (tpp80) REVERT: B 43 GLN cc_start: 0.8150 (mt0) cc_final: 0.7718 (mp10) REVERT: I 346 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7662 (mtm-85) outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.5977 time to fit residues: 29.4368 Evaluate side-chains 45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain I residue 441 LEU Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.0470 chunk 36 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 33 optimal weight: 0.4980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 354 ASN I 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.158959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.149586 restraints weight = 4175.122| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.12 r_work: 0.3519 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3194 Z= 0.170 Angle : 0.584 9.174 4358 Z= 0.293 Chirality : 0.045 0.140 479 Planarity : 0.005 0.053 553 Dihedral : 4.268 18.511 531 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.81 % Allowed : 16.49 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.16 (0.40), residues: 396 helix: -3.53 (0.67), residues: 33 sheet: 0.30 (0.43), residues: 144 loop : -1.05 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 62 TYR 0.018 0.001 TYR A 95 PHE 0.011 0.001 PHE I 392 TRP 0.009 0.002 TRP A 117 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 3185) covalent geometry : angle 0.57965 ( 4336) SS BOND : bond 0.00312 ( 5) SS BOND : angle 0.88536 ( 10) hydrogen bonds : bond 0.03873 ( 116) hydrogen bonds : angle 5.97496 ( 282) link_BETA1-4 : bond 0.00403 ( 2) link_BETA1-4 : angle 1.49909 ( 6) link_BETA1-6 : bond 0.00042 ( 1) link_BETA1-6 : angle 1.42714 ( 3) link_NAG-ASN : bond 0.00201 ( 1) link_NAG-ASN : angle 0.99901 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1444.91 seconds wall clock time: 25 minutes 19.75 seconds (1519.75 seconds total)