Starting phenix.real_space_refine on Wed Jul 1 22:04:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tly_25990/07_2026/7tly_25990.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tly_25990/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tly_25990/07_2026/7tly_25990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tly_25990/07_2026/7tly_25990.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tly_25990/07_2026/7tly_25990.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tly_25990/07_2026/7tly_25990.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tly_25990/07_2026/7tly_25990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tly_25990/07_2026/7tly_25990.cif" } 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-6108/lib/python3.11/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 chiralities: 4 Time building chain proxies: 0.91, per 1000 atoms: 0.29 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: 0.37 Conformation dependent library (CDL) restraints added in 118.1 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: 0.11 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: 0.43 Time building geometry restraints manager: 0.42 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 - 17.52: 1746 17.52 - 35.03: 53 35.03 - 52.54: 13 52.54 - 70.05: 6 70.05 - 87.56: 1 Dihedral angle restraints: 1819 sinusoidal: 646 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 1816 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: 9.330 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.940 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 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 : 9.972 87.564 1060 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/Z covalent geometry : bond 0.00998 / 0.56 ( 3185) covalent geometry : angle 1.32024 / 0.89 ( 4336) SS BOND : bond 0.03371 / 2.28 ( 5) SS BOND : angle 2.51708 / 1.49 ( 10) hydrogen bonds : bond 0.17018 / 11.38 ( 116) hydrogen bonds : angle 8.84395 / 6.13 ( 282) link_BETA1-4 : bond 0.05749 / 2.90 ( 2) link_BETA1-4 : angle 2.55125 / 1.43 ( 6) link_BETA1-6 : bond 0.04853 / 2.55 ( 1) link_BETA1-6 : angle 1.46037 / 0.74 ( 3) link_NAG-ASN : bond 0.05745 / 3.02 ( 1) link_NAG-ASN : angle 2.44605 / 1.24 ( 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 : 0.126 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: 0.4954 time to fit residues: 32.5907 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 : 0.111 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.165231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.153926 restraints weight = 4168.720| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.38 r_work: 0.3576 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3194 Z= 0.181 Angle : 0.620 8.674 4358 Z= 0.326 Chirality : 0.048 0.163 479 Planarity : 0.006 0.051 553 Dihedral : 4.435 15.141 453 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.21 % Allowed : 8.42 % 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: -0.06 (0.40), residues: 396 helix: -2.86 (0.82), residues: 33 sheet: 0.63 (0.40), residues: 153 loop : 0.04 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 457 TYR 0.012 0.002 TYR A 94 PHE 0.013 0.002 PHE I 497 TRP 0.012 0.002 TRP A 117 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 3185) covalent geometry : angle 0.61402 / 0.32 ( 4336) SS BOND : bond 0.00423 / 0.27 ( 5) SS BOND : angle 1.09321 / 0.63 ( 10) hydrogen bonds : bond 0.04707 / 3.08 ( 116) hydrogen bonds : angle 6.68585 / 4.69 ( 282) link_BETA1-4 : bond 0.00405 / 0.20 ( 2) link_BETA1-4 : angle 1.50087 / 0.72 ( 6) link_BETA1-6 : bond 0.00482 / 0.25 ( 1) link_BETA1-6 : angle 1.37498 / 0.71 ( 3) link_NAG-ASN : bond 0.00750 / 0.39 ( 1) link_NAG-ASN : angle 1.55312 / 0.80 ( 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 61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.070 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.7013 (mm-40) REVERT: A 59 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7802 (t0) REVERT: B 24 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7532 (mtp85) REVERT: B 43 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7839 (mt0) outliers start: 12 outliers final: 3 residues processed: 55 average time/residue: 0.4007 time to fit residues: 22.6482 Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B 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: 1.9990 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 13 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.161606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.151884 restraints weight = 4129.037| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.13 r_work: 0.3557 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3095 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= 0.169 Angle : 0.590 9.197 4358 Z= 0.303 Chirality : 0.046 0.152 479 Planarity : 0.005 0.050 553 Dihedral : 4.404 16.321 453 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.11 % Allowed : 12.98 % Favored : 84.91 % 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: -0.30 (0.40), residues: 396 helix: -2.45 (1.01), residues: 26 sheet: 0.57 (0.42), residues: 140 loop : -0.37 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.020 0.002 TYR A 95 PHE 0.011 0.002 PHE I 429 TRP 0.009 0.002 TRP A 50 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 3185) covalent geometry : angle 0.58524 / 0.30 ( 4336) SS BOND : bond 0.00367 / 0.23 ( 5) SS BOND : angle 1.00711 / 0.61 ( 10) hydrogen bonds : bond 0.04278 / 2.77 ( 116) hydrogen bonds : angle 6.23776 / 4.32 ( 282) link_BETA1-4 : bond 0.00595 / 0.30 ( 2) link_BETA1-4 : angle 1.27759 / 0.70 ( 6) link_BETA1-6 : bond 0.00390 / 0.21 ( 1) link_BETA1-6 : angle 1.43272 / 0.73 ( 3) link_NAG-ASN : bond 0.00474 / 0.25 ( 1) link_NAG-ASN : angle 1.08409 / 0.60 ( 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 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.117 Fit side-chains REVERT: A 59 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7795 (t0) REVERT: B 24 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7510 (mtp85) REVERT: I 457 ARG cc_start: 0.8093 (ttt90) cc_final: 0.7729 (ttt90) outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 0.5987 time to fit residues: 30.1077 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain B residue 24 ARG 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: 0.3980 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.157517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.147321 restraints weight = 4088.467| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.18 r_work: 0.3499 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3194 Z= 0.246 Angle : 0.696 10.567 4358 Z= 0.349 Chirality : 0.049 0.154 479 Planarity : 0.006 0.055 553 Dihedral : 4.877 18.905 453 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.61 % Allowed : 9.82 % 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: -1.03 (0.39), residues: 396 helix: -3.20 (0.77), residues: 32 sheet: 0.19 (0.41), residues: 143 loop : -0.84 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 62 TYR 0.023 0.002 TYR A 95 PHE 0.014 0.002 PHE I 429 TRP 0.014 0.002 TRP A 50 HIS 0.003 0.002 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.25 ( 3185) covalent geometry : angle 0.69090 / 0.35 ( 4336) SS BOND : bond 0.00341 / 0.20 ( 5) SS BOND : angle 1.23750 / 0.77 ( 10) hydrogen bonds : bond 0.04817 / 3.10 ( 116) hydrogen bonds : angle 6.46059 / 4.49 ( 282) link_BETA1-4 : bond 0.00491 / 0.25 ( 2) link_BETA1-4 : angle 1.42471 / 0.78 ( 6) link_BETA1-6 : bond 0.00073 / 0.04 ( 1) link_BETA1-6 : angle 1.70615 / 0.87 ( 3) link_NAG-ASN : bond 0.00250 / 0.13 ( 1) link_NAG-ASN : angle 1.06258 / 0.57 ( 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 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.116 Fit side-chains REVERT: A 59 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8001 (t0) REVERT: A 99 ASP cc_start: 0.8775 (t70) cc_final: 0.8556 (t70) REVERT: A 119 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.6597 (pm20) REVERT: B 24 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7514 (mtp85) REVERT: I 346 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7706 (ttm-80) outliers start: 16 outliers final: 7 residues processed: 50 average time/residue: 0.5658 time to fit residues: 29.0936 Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 24 ARG 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 514 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.0010 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.158031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.148488 restraints weight = 4115.260| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.13 r_work: 0.3517 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3194 Z= 0.202 Angle : 0.631 11.320 4358 Z= 0.317 Chirality : 0.047 0.140 479 Planarity : 0.006 0.059 553 Dihedral : 4.637 18.441 453 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.21 % Allowed : 10.18 % Favored : 85.61 % 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: -1.19 (0.39), residues: 396 helix: -3.28 (0.75), residues: 32 sheet: 0.17 (0.42), residues: 143 loop : -1.04 (0.36), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 62 TYR 0.021 0.002 TYR A 95 PHE 0.010 0.001 PHE I 429 TRP 0.008 0.002 TRP A 50 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 ( 3185) covalent geometry : angle 0.62664 / 0.32 ( 4336) SS BOND : bond 0.00301 / 0.17 ( 5) SS BOND : angle 1.04256 / 0.65 ( 10) hydrogen bonds : bond 0.04361 / 2.75 ( 116) hydrogen bonds : angle 6.35265 / 4.42 ( 282) link_BETA1-4 : bond 0.00461 / 0.23 ( 2) link_BETA1-4 : angle 1.46570 / 0.80 ( 6) link_BETA1-6 : bond 0.00021 / 0.01 ( 1) link_BETA1-6 : angle 1.56434 / 0.78 ( 3) link_NAG-ASN : bond 0.00217 / 0.11 ( 1) link_NAG-ASN : angle 1.08082 / 0.59 ( 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 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.145 Fit side-chains REVERT: A 59 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.7933 (t0) REVERT: B 24 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7477 (mtp85) REVERT: I 346 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7581 (mtm-85) outliers start: 12 outliers final: 7 residues processed: 51 average time/residue: 0.5827 time to fit residues: 30.5992 Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 24 ARG 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: 0.6980 chunk 38 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.157070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.147583 restraints weight = 4154.475| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.12 r_work: 0.3503 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3194 Z= 0.220 Angle : 0.651 11.518 4358 Z= 0.325 Chirality : 0.048 0.147 479 Planarity : 0.006 0.056 553 Dihedral : 4.660 18.903 453 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.91 % Allowed : 11.93 % Favored : 83.16 % 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: -1.38 (0.39), residues: 396 helix: -3.31 (0.72), residues: 33 sheet: 0.09 (0.43), residues: 144 loop : -1.22 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 62 TYR 0.022 0.002 TYR A 95 PHE 0.011 0.002 PHE I 392 TRP 0.011 0.002 TRP A 50 HIS 0.003 0.002 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 ( 3185) covalent geometry : angle 0.64653 / 0.32 ( 4336) SS BOND : bond 0.00339 / 0.20 ( 5) SS BOND : angle 1.11083 / 0.71 ( 10) hydrogen bonds : bond 0.04495 / 2.84 ( 116) hydrogen bonds : angle 6.39160 / 4.46 ( 282) link_BETA1-4 : bond 0.00498 / 0.25 ( 2) link_BETA1-4 : angle 1.50785 / 0.84 ( 6) link_BETA1-6 : bond 0.00026 / 0.01 ( 1) link_BETA1-6 : angle 1.63106 / 0.81 ( 3) link_NAG-ASN : bond 0.00234 / 0.12 ( 1) link_NAG-ASN : angle 1.04629 / 0.56 ( 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 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.122 Fit side-chains REVERT: A 119 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.6771 (pm20) REVERT: B 24 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7519 (mtp85) REVERT: I 346 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7653 (mtm-85) outliers start: 14 outliers final: 9 residues processed: 49 average time/residue: 0.5792 time to fit residues: 29.1560 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 24 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.156737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.147138 restraints weight = 4188.229| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.15 r_work: 0.3500 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4225 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= 0.233 Angle : 0.665 11.649 4358 Z= 0.332 Chirality : 0.048 0.149 479 Planarity : 0.007 0.058 553 Dihedral : 4.667 19.157 453 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.56 % Allowed : 13.33 % 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: -1.52 (0.39), residues: 396 helix: -3.33 (0.72), residues: 33 sheet: 0.04 (0.43), residues: 144 loop : -1.36 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 62 TYR 0.022 0.002 TYR A 95 PHE 0.010 0.002 PHE I 429 TRP 0.011 0.002 TRP A 50 HIS 0.003 0.002 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 ( 3185) covalent geometry : angle 0.65921 / 0.33 ( 4336) SS BOND : bond 0.00355 / 0.20 ( 5) SS BOND : angle 1.15869 / 0.73 ( 10) hydrogen bonds : bond 0.04607 / 2.90 ( 116) hydrogen bonds : angle 6.45820 / 4.50 ( 282) link_BETA1-4 : bond 0.00530 / 0.27 ( 2) link_BETA1-4 : angle 1.58302 / 0.89 ( 6) link_BETA1-6 : bond 0.00009 / 0.00 ( 1) link_BETA1-6 : angle 1.69030 / 0.84 ( 3) link_NAG-ASN : bond 0.00174 / 0.09 ( 1) link_NAG-ASN : angle 1.01728 / 0.55 ( 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 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.117 Fit side-chains REVERT: B 24 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7513 (mtp85) REVERT: I 346 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7697 (mtm-85) REVERT: I 465 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7735 (tt0) outliers start: 13 outliers final: 9 residues processed: 48 average time/residue: 0.5582 time to fit residues: 27.5827 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 24 ARG 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: 0.8980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.0870 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.0570 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 overall best weight: 0.5276 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.156835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.146751 restraints weight = 4277.689| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.21 r_work: 0.3486 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4286 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= 0.214 Angle : 0.649 11.304 4358 Z= 0.323 Chirality : 0.048 0.147 479 Planarity : 0.006 0.056 553 Dihedral : 4.546 19.037 453 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.56 % Allowed : 14.39 % Favored : 81.05 % 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: -1.55 (0.39), residues: 396 helix: -3.42 (0.69), residues: 33 sheet: 0.01 (0.43), residues: 144 loop : -1.36 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 62 TYR 0.021 0.002 TYR A 95 PHE 0.011 0.002 PHE I 392 TRP 0.009 0.002 TRP A 117 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 ( 3185) covalent geometry : angle 0.64418 / 0.32 ( 4336) SS BOND : bond 0.00313 / 0.18 ( 5) SS BOND : angle 1.07398 / 0.68 ( 10) hydrogen bonds : bond 0.04400 / 2.80 ( 116) hydrogen bonds : angle 6.37649 / 4.45 ( 282) link_BETA1-4 : bond 0.00479 / 0.24 ( 2) link_BETA1-4 : angle 1.61104 / 0.91 ( 6) link_BETA1-6 : bond 0.00034 / 0.02 ( 1) link_BETA1-6 : angle 1.66979 / 0.83 ( 3) link_NAG-ASN : bond 0.00138 / 0.07 ( 1) link_NAG-ASN : angle 1.04625 / 0.58 ( 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 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.126 Fit side-chains REVERT: A 119 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7022 (pm20) REVERT: B 24 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7531 (mtp85) REVERT: I 346 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7671 (mtm-85) outliers start: 13 outliers final: 9 residues processed: 47 average time/residue: 0.5877 time to fit residues: 28.4222 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 : 0.116 ------------------------------------------------------------------------------- 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 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 24 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 13 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.157232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.147271 restraints weight = 4211.289| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.21 r_work: 0.3499 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3194 Z= 0.196 Angle : 0.631 10.924 4358 Z= 0.314 Chirality : 0.047 0.144 479 Planarity : 0.006 0.056 553 Dihedral : 4.489 18.725 453 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.56 % Allowed : 15.09 % Favored : 80.35 % 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: -1.53 (0.39), residues: 396 helix: -3.42 (0.69), residues: 33 sheet: 0.03 (0.43), residues: 144 loop : -1.36 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 62 TYR 0.021 0.002 TYR A 95 PHE 0.008 0.001 PHE I 429 TRP 0.011 0.002 TRP A 50 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 3185) covalent geometry : angle 0.62620 / 0.31 ( 4336) SS BOND : bond 0.00317 / 0.18 ( 5) SS BOND : angle 1.02725 / 0.65 ( 10) hydrogen bonds : bond 0.04261 / 2.69 ( 116) hydrogen bonds : angle 6.34961 / 4.42 ( 282) link_BETA1-4 : bond 0.00511 / 0.26 ( 2) link_BETA1-4 : angle 1.64679 / 0.93 ( 6) link_BETA1-6 : bond 0.00034 / 0.02 ( 1) link_BETA1-6 : angle 1.57912 / 0.78 ( 3) link_NAG-ASN : bond 0.00150 / 0.08 ( 1) link_NAG-ASN : angle 1.03250 / 0.58 ( 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 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.119 Fit side-chains REVERT: A 59 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.7975 (t0) REVERT: A 90 ASP cc_start: 0.6888 (m-30) cc_final: 0.6301 (m-30) REVERT: A 119 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7012 (pm20) REVERT: B 24 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7497 (mtp85) REVERT: I 346 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7685 (mtm-85) REVERT: I 465 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7736 (tt0) outliers start: 13 outliers final: 8 residues processed: 47 average time/residue: 0.6011 time to fit residues: 29.0676 Evaluate side-chains 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 24 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 0.4980 chunk 36 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 22 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.0980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.158076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.148141 restraints weight = 4146.122| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.20 r_work: 0.3506 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3194 Z= 0.156 Angle : 0.579 9.753 4358 Z= 0.288 Chirality : 0.045 0.139 479 Planarity : 0.006 0.055 553 Dihedral : 4.259 18.136 453 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.21 % Allowed : 15.44 % Favored : 80.35 % 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: -1.42 (0.40), residues: 396 helix: -3.39 (0.69), residues: 33 sheet: 0.09 (0.44), residues: 144 loop : -1.26 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 62 TYR 0.020 0.001 TYR A 95 PHE 0.006 0.001 PHE I 429 TRP 0.013 0.002 TRP A 50 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 3185) covalent geometry : angle 0.57333 / 0.29 ( 4336) SS BOND : bond 0.00263 / 0.15 ( 5) SS BOND : angle 0.89490 / 0.56 ( 10) hydrogen bonds : bond 0.03901 / 2.44 ( 116) hydrogen bonds : angle 6.18060 / 4.31 ( 282) link_BETA1-4 : bond 0.00472 / 0.24 ( 2) link_BETA1-4 : angle 1.62347 / 0.91 ( 6) link_BETA1-6 : bond 0.00079 / 0.04 ( 1) link_BETA1-6 : angle 1.50886 / 0.75 ( 3) link_NAG-ASN : bond 0.00157 / 0.08 ( 1) link_NAG-ASN : angle 1.06240 / 0.60 ( 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 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.117 Fit side-chains REVERT: A 90 ASP cc_start: 0.6826 (m-30) cc_final: 0.6244 (m-30) REVERT: A 119 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: B 24 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7459 (mtp85) REVERT: I 346 ARG cc_start: 0.7983 (ttm-80) cc_final: 0.7665 (mtm-85) REVERT: I 465 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7741 (tt0) outliers start: 12 outliers final: 7 residues processed: 47 average time/residue: 0.5326 time to fit residues: 25.8075 Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 24 ARG 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 465 GLU 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: 0.3980 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.156155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.146094 restraints weight = 4211.803| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.21 r_work: 0.3479 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3194 Z= 0.259 Angle : 0.704 11.548 4358 Z= 0.350 Chirality : 0.050 0.151 479 Planarity : 0.006 0.057 553 Dihedral : 4.687 19.472 453 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.86 % Allowed : 15.79 % Favored : 80.35 % 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: -1.61 (0.39), residues: 396 helix: -3.51 (0.65), residues: 34 sheet: 0.02 (0.44), residues: 143 loop : -1.42 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 62 TYR 0.022 0.002 TYR A 95 PHE 0.010 0.002 PHE I 429 TRP 0.009 0.002 TRP A 117 HIS 0.004 0.002 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.26 ( 3185) covalent geometry : angle 0.69842 / 0.35 ( 4336) SS BOND : bond 0.00384 / 0.22 ( 5) SS BOND : angle 1.22306 / 0.78 ( 10) hydrogen bonds : bond 0.04711 / 3.01 ( 116) hydrogen bonds : angle 6.50245 / 4.52 ( 282) link_BETA1-4 : bond 0.00541 / 0.27 ( 2) link_BETA1-4 : angle 1.76012 / 1.01 ( 6) link_BETA1-6 : bond 0.00151 / 0.08 ( 1) link_BETA1-6 : angle 1.75782 / 0.86 ( 3) link_NAG-ASN : bond 0.00158 / 0.08 ( 1) link_NAG-ASN : angle 0.88319 / 0.49 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1449.65 seconds wall clock time: 25 minutes 31.11 seconds (1531.11 seconds total)