Starting phenix.real_space_refine on Tue Mar 3 14:47:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x90_33062/03_2026/7x90_33062_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x90_33062/03_2026/7x90_33062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x90_33062/03_2026/7x90_33062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x90_33062/03_2026/7x90_33062.map" model { file = "/net/cci-nas-00/data/ceres_data/7x90_33062/03_2026/7x90_33062_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x90_33062/03_2026/7x90_33062_trim.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 16 5.16 5 C 2092 2.51 5 N 560 2.21 5 O 633 1.98 5 H 3140 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 6441 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1816 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1609 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "G" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.27, per 1000 atoms: 0.20 Number of scatterers: 6441 At special positions: 0 Unit cell: (98.651, 71.294, 71.294, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 O 633 8.00 N 560 7.00 C 2092 6.00 H 3140 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN G 343 " Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 253.6 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 6 sheets defined 5.0% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 337 through 341 Processing helix chain 'G' and resid 366 through 371 removed outlier: 3.624A pdb=" N SER G 371 " --> pdb=" O VAL G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 410 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.571A pdb=" N GLY E 10 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.779A pdb=" N VAL F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR F 72 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER F 65 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.664A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN F 38 " --> pdb=" O ALA F 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 356 through 358 removed outlier: 3.779A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 361 through 362 removed outlier: 6.827A pdb=" N CYS G 361 " --> pdb=" O CYS G 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 74 hydrogen bonds defined for protein. 168 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: 1.00 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3140 1.03 - 1.23: 18 1.23 - 1.43: 1484 1.43 - 1.62: 1862 1.62 - 1.82: 20 Bond restraints: 6524 Sorted by residual: bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" N ASP F 1 " pdb=" H ASP F 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.99e+00 bond pdb=" C THR F 94 " pdb=" N PRO F 95 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.30e-02 5.92e+03 1.57e+00 ... (remaining 6519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 10928 1.07 - 2.14: 690 2.14 - 3.21: 42 3.21 - 4.27: 14 4.27 - 5.34: 4 Bond angle restraints: 11678 Sorted by residual: angle pdb=" C SER F 30 " pdb=" CA SER F 30 " pdb=" CB SER F 30 " ideal model delta sigma weight residual 110.42 115.76 -5.34 1.99e+00 2.53e-01 7.21e+00 angle pdb=" N SER F 30 " pdb=" CA SER F 30 " pdb=" C SER F 30 " ideal model delta sigma weight residual 110.80 106.54 4.26 2.13e+00 2.20e-01 3.99e+00 angle pdb=" CA SER F 30 " pdb=" C SER F 30 " pdb=" N ASN F 31 " ideal model delta sigma weight residual 116.84 119.83 -2.99 1.71e+00 3.42e-01 3.06e+00 angle pdb=" N THR F 94 " pdb=" CA THR F 94 " pdb=" C THR F 94 " ideal model delta sigma weight residual 109.81 113.40 -3.59 2.21e+00 2.05e-01 2.63e+00 angle pdb=" C TYR G 508 " pdb=" N ARG G 509 " pdb=" CA ARG G 509 " ideal model delta sigma weight residual 122.30 120.12 2.18 1.35e+00 5.49e-01 2.62e+00 ... (remaining 11673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.68: 2768 14.68 - 29.36: 250 29.36 - 44.04: 116 44.04 - 58.72: 43 58.72 - 73.39: 5 Dihedral angle restraints: 3182 sinusoidal: 1702 harmonic: 1480 Sorted by residual: dihedral pdb=" CA CYS G 336 " pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " ideal model delta sinusoidal sigma weight residual -73.00 -7.14 -65.86 1 2.00e+01 2.50e-03 1.42e+01 dihedral pdb=" CA GLU G 516 " pdb=" C GLU G 516 " pdb=" N LEU G 517 " pdb=" CA LEU G 517 " ideal model delta harmonic sigma weight residual -180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB CYS G 391 " pdb=" SG CYS G 391 " pdb=" SG CYS G 525 " pdb=" CB CYS G 525 " ideal model delta sinusoidal sigma weight residual -86.00 -58.36 -27.64 1 1.00e+01 1.00e-02 1.10e+01 ... (remaining 3179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 329 0.034 - 0.068: 119 0.068 - 0.101: 39 0.101 - 0.135: 14 0.135 - 0.169: 1 Chirality restraints: 502 Sorted by residual: chirality pdb=" CA ILE G 434 " pdb=" N ILE G 434 " pdb=" C ILE G 434 " pdb=" CB ILE G 434 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA ILE F 21 " pdb=" N ILE F 21 " pdb=" C ILE F 21 " pdb=" CB ILE F 21 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL G 511 " pdb=" N VAL G 511 " pdb=" C VAL G 511 " pdb=" CB VAL G 511 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 499 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 32 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO E 33 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 33 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 33 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN G 506 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO G 507 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 507 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 507 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 508 " -0.000 2.00e-02 2.50e+03 5.50e-03 9.07e-01 pdb=" CG TYR G 508 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR G 508 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR G 508 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR G 508 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR G 508 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR G 508 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 508 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR G 508 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR G 508 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR G 508 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR G 508 " -0.001 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 380 2.18 - 2.78: 12634 2.78 - 3.39: 16304 3.39 - 3.99: 21120 3.99 - 4.60: 31957 Nonbonded interactions: 82395 Sorted by model distance: nonbonded pdb=" O GLN F 79 " pdb=" H GLU F 81 " model vdw 1.575 2.450 nonbonded pdb=" OE2 GLU E 6 " pdb=" H GLY E 113 " model vdw 1.603 2.450 nonbonded pdb="HH21 ARG G 403 " pdb=" OE1 GLU G 406 " model vdw 1.651 2.450 nonbonded pdb=" O VAL G 503 " pdb="HE21 GLN G 506 " model vdw 1.671 2.450 nonbonded pdb=" O SER F 30 " pdb=" H GLY F 68 " model vdw 1.687 2.450 ... (remaining 82390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 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: 0.030 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.520 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 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 : 0.003 0.033 3392 Z= 0.137 Angle : 0.581 5.343 4618 Z= 0.305 Chirality : 0.042 0.169 502 Planarity : 0.003 0.033 595 Dihedral : 13.963 73.394 1235 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.37), residues: 414 helix: -3.48 (1.39), residues: 12 sheet: -0.39 (0.47), residues: 111 loop : -2.90 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 509 TYR 0.012 0.001 TYR G 508 PHE 0.005 0.001 PHE G 456 TRP 0.008 0.001 TRP F 35 HIS 0.005 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3384) covalent geometry : angle 0.57935 ( 4600) SS BOND : bond 0.00370 ( 6) SS BOND : angle 0.71117 ( 12) hydrogen bonds : bond 0.11659 ( 74) hydrogen bonds : angle 7.02936 ( 168) link_BETA1-4 : bond 0.00173 ( 1) link_BETA1-4 : angle 0.84138 ( 3) link_NAG-ASN : bond 0.00081 ( 1) link_NAG-ASN : angle 1.51062 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1716 time to fit residues: 23.1975 Evaluate side-chains 80 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 0.0370 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.075037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.061961 restraints weight = 36455.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.065627 restraints weight = 15993.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068224 restraints weight = 8803.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.069993 restraints weight = 5397.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.071184 restraints weight = 3550.710| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3392 Z= 0.125 Angle : 0.546 5.844 4618 Z= 0.286 Chirality : 0.042 0.152 502 Planarity : 0.004 0.035 595 Dihedral : 5.944 51.595 507 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.37), residues: 414 helix: -2.09 (1.28), residues: 18 sheet: -0.48 (0.46), residues: 117 loop : -2.92 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 457 TYR 0.006 0.001 TYR G 453 PHE 0.013 0.001 PHE F 71 TRP 0.005 0.001 TRP G 353 HIS 0.005 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3384) covalent geometry : angle 0.54440 ( 4600) SS BOND : bond 0.00376 ( 6) SS BOND : angle 0.62670 ( 12) hydrogen bonds : bond 0.03263 ( 74) hydrogen bonds : angle 6.19337 ( 168) link_BETA1-4 : bond 0.00076 ( 1) link_BETA1-4 : angle 0.82485 ( 3) link_NAG-ASN : bond 0.00036 ( 1) link_NAG-ASN : angle 1.21984 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 354 ASN cc_start: 0.9503 (m110) cc_final: 0.9283 (m-40) REVERT: G 389 ASP cc_start: 0.9214 (m-30) cc_final: 0.8945 (m-30) REVERT: G 516 GLU cc_start: 0.8586 (mt-10) cc_final: 0.7997 (mt-10) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1663 time to fit residues: 17.4692 Evaluate side-chains 75 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN G 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.072999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.059964 restraints weight = 37324.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.063641 restraints weight = 16488.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.066116 restraints weight = 9041.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.067868 restraints weight = 5592.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.069059 restraints weight = 3736.748| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3392 Z= 0.156 Angle : 0.555 5.827 4618 Z= 0.291 Chirality : 0.041 0.145 502 Planarity : 0.004 0.028 595 Dihedral : 5.687 50.167 507 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.37), residues: 414 helix: -2.20 (1.23), residues: 18 sheet: -0.64 (0.45), residues: 124 loop : -2.84 (0.32), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 87 TYR 0.007 0.001 TYR G 453 PHE 0.018 0.001 PHE F 71 TRP 0.009 0.001 TRP F 35 HIS 0.005 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3384) covalent geometry : angle 0.55382 ( 4600) SS BOND : bond 0.00320 ( 6) SS BOND : angle 0.64724 ( 12) hydrogen bonds : bond 0.02986 ( 74) hydrogen bonds : angle 5.83818 ( 168) link_BETA1-4 : bond 0.00046 ( 1) link_BETA1-4 : angle 1.19708 ( 3) link_NAG-ASN : bond 0.00062 ( 1) link_NAG-ASN : angle 1.20109 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8725 (pt0) REVERT: E 102 MET cc_start: 0.8938 (mmm) cc_final: 0.8689 (mmm) REVERT: F 11 LEU cc_start: 0.9207 (pp) cc_final: 0.8922 (pp) REVERT: F 29 ILE cc_start: 0.9510 (mm) cc_final: 0.9299 (mm) REVERT: G 354 ASN cc_start: 0.9494 (m110) cc_final: 0.9282 (m-40) REVERT: G 389 ASP cc_start: 0.9207 (m-30) cc_final: 0.8938 (m-30) REVERT: G 467 ASP cc_start: 0.7173 (t0) cc_final: 0.6873 (t0) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1716 time to fit residues: 18.4938 Evaluate side-chains 76 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.073640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.060486 restraints weight = 37119.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.064129 restraints weight = 16319.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.066669 restraints weight = 8969.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.068400 restraints weight = 5532.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.069623 restraints weight = 3710.316| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3392 Z= 0.109 Angle : 0.554 5.657 4618 Z= 0.288 Chirality : 0.042 0.147 502 Planarity : 0.004 0.037 595 Dihedral : 5.579 51.526 507 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.63 % Favored : 89.13 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.37), residues: 414 helix: -2.17 (1.25), residues: 18 sheet: -0.23 (0.48), residues: 114 loop : -2.81 (0.32), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 87 TYR 0.010 0.001 TYR F 92 PHE 0.016 0.001 PHE G 400 TRP 0.019 0.001 TRP F 35 HIS 0.003 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3384) covalent geometry : angle 0.55271 ( 4600) SS BOND : bond 0.00373 ( 6) SS BOND : angle 0.69505 ( 12) hydrogen bonds : bond 0.02933 ( 74) hydrogen bonds : angle 5.73022 ( 168) link_BETA1-4 : bond 0.00090 ( 1) link_BETA1-4 : angle 0.88516 ( 3) link_NAG-ASN : bond 0.00194 ( 1) link_NAG-ASN : angle 0.96979 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8762 (pt0) REVERT: E 102 MET cc_start: 0.8895 (mmm) cc_final: 0.8680 (mmm) REVERT: G 354 ASN cc_start: 0.9498 (m110) cc_final: 0.9285 (m-40) REVERT: G 389 ASP cc_start: 0.9202 (m-30) cc_final: 0.8936 (m-30) REVERT: G 467 ASP cc_start: 0.7179 (t0) cc_final: 0.6923 (t0) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1617 time to fit residues: 16.8214 Evaluate side-chains 73 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.072202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.059075 restraints weight = 37269.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062634 restraints weight = 16458.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.065114 restraints weight = 9109.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.066852 restraints weight = 5662.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068023 restraints weight = 3824.695| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3392 Z= 0.150 Angle : 0.549 5.526 4618 Z= 0.286 Chirality : 0.041 0.143 502 Planarity : 0.004 0.033 595 Dihedral : 5.500 50.725 507 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.04 % Favored : 86.71 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.37), residues: 414 helix: -2.26 (1.21), residues: 18 sheet: -0.58 (0.46), residues: 124 loop : -2.74 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 87 TYR 0.009 0.001 TYR F 92 PHE 0.012 0.001 PHE F 71 TRP 0.012 0.001 TRP F 35 HIS 0.004 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 3384) covalent geometry : angle 0.54719 ( 4600) SS BOND : bond 0.00391 ( 6) SS BOND : angle 0.68530 ( 12) hydrogen bonds : bond 0.02945 ( 74) hydrogen bonds : angle 5.69560 ( 168) link_BETA1-4 : bond 0.00084 ( 1) link_BETA1-4 : angle 1.23300 ( 3) link_NAG-ASN : bond 0.00077 ( 1) link_NAG-ASN : angle 1.14479 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8780 (pt0) REVERT: F 100 GLN cc_start: 0.9408 (mp10) cc_final: 0.9118 (mp10) REVERT: G 354 ASN cc_start: 0.9515 (m110) cc_final: 0.9310 (m-40) REVERT: G 389 ASP cc_start: 0.9181 (m-30) cc_final: 0.8916 (m-30) REVERT: G 467 ASP cc_start: 0.7194 (t0) cc_final: 0.6925 (t0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1622 time to fit residues: 16.6369 Evaluate side-chains 74 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN F 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.072960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.060094 restraints weight = 36326.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.063703 restraints weight = 15679.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.066178 restraints weight = 8536.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067937 restraints weight = 5268.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.069111 restraints weight = 3467.673| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3392 Z= 0.096 Angle : 0.519 5.494 4618 Z= 0.269 Chirality : 0.042 0.147 502 Planarity : 0.004 0.031 595 Dihedral : 5.343 51.664 507 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.90 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.37), residues: 414 helix: -2.09 (1.27), residues: 18 sheet: -0.35 (0.47), residues: 115 loop : -2.70 (0.32), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 87 TYR 0.006 0.001 TYR F 36 PHE 0.011 0.001 PHE G 400 TRP 0.007 0.001 TRP F 35 HIS 0.003 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 3384) covalent geometry : angle 0.51800 ( 4600) SS BOND : bond 0.00326 ( 6) SS BOND : angle 0.74447 ( 12) hydrogen bonds : bond 0.02762 ( 74) hydrogen bonds : angle 5.53979 ( 168) link_BETA1-4 : bond 0.00259 ( 1) link_BETA1-4 : angle 0.88331 ( 3) link_NAG-ASN : bond 0.00260 ( 1) link_NAG-ASN : angle 0.84163 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8795 (pt0) REVERT: F 86 TYR cc_start: 0.9076 (m-10) cc_final: 0.8783 (m-10) REVERT: F 100 GLN cc_start: 0.9395 (mp10) cc_final: 0.9119 (mp10) REVERT: G 354 ASN cc_start: 0.9512 (m110) cc_final: 0.9305 (m-40) REVERT: G 389 ASP cc_start: 0.9165 (m-30) cc_final: 0.8905 (m-30) REVERT: G 467 ASP cc_start: 0.7155 (t0) cc_final: 0.6874 (t0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1689 time to fit residues: 17.5717 Evaluate side-chains 75 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.072934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.059936 restraints weight = 36342.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.063510 restraints weight = 15829.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.066014 restraints weight = 8727.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.067799 restraints weight = 5373.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.068974 restraints weight = 3568.253| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3392 Z= 0.107 Angle : 0.519 5.487 4618 Z= 0.268 Chirality : 0.041 0.141 502 Planarity : 0.004 0.033 595 Dihedral : 5.292 51.557 507 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.35 % Favored : 88.41 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.37), residues: 414 helix: -2.09 (1.27), residues: 18 sheet: -0.45 (0.46), residues: 118 loop : -2.77 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 87 TYR 0.006 0.001 TYR F 86 PHE 0.008 0.001 PHE F 71 TRP 0.009 0.001 TRP F 35 HIS 0.003 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 3384) covalent geometry : angle 0.51746 ( 4600) SS BOND : bond 0.00410 ( 6) SS BOND : angle 0.79381 ( 12) hydrogen bonds : bond 0.02814 ( 74) hydrogen bonds : angle 5.49538 ( 168) link_BETA1-4 : bond 0.00189 ( 1) link_BETA1-4 : angle 1.04237 ( 3) link_NAG-ASN : bond 0.00189 ( 1) link_NAG-ASN : angle 1.00162 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8831 (pt0) REVERT: F 100 GLN cc_start: 0.9385 (mp10) cc_final: 0.9120 (mp10) REVERT: G 354 ASN cc_start: 0.9525 (m110) cc_final: 0.9300 (m-40) REVERT: G 389 ASP cc_start: 0.9169 (m-30) cc_final: 0.8912 (m-30) REVERT: G 467 ASP cc_start: 0.7175 (t0) cc_final: 0.6945 (t0) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1384 time to fit residues: 14.0898 Evaluate side-chains 74 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.3980 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.072631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.059035 restraints weight = 36389.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.062750 restraints weight = 15975.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.065361 restraints weight = 8845.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.067137 restraints weight = 5469.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068441 restraints weight = 3671.826| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3392 Z= 0.101 Angle : 0.521 5.516 4618 Z= 0.270 Chirality : 0.042 0.140 502 Planarity : 0.004 0.031 595 Dihedral : 5.233 51.666 507 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.42 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.37), residues: 414 helix: -2.67 (0.96), residues: 25 sheet: -0.45 (0.46), residues: 118 loop : -2.69 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 87 TYR 0.005 0.001 TYR G 396 PHE 0.008 0.001 PHE G 400 TRP 0.005 0.001 TRP F 35 HIS 0.003 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 3384) covalent geometry : angle 0.51954 ( 4600) SS BOND : bond 0.00378 ( 6) SS BOND : angle 0.78490 ( 12) hydrogen bonds : bond 0.02616 ( 74) hydrogen bonds : angle 5.42812 ( 168) link_BETA1-4 : bond 0.00144 ( 1) link_BETA1-4 : angle 0.95133 ( 3) link_NAG-ASN : bond 0.00213 ( 1) link_NAG-ASN : angle 0.94837 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 100 GLN cc_start: 0.9354 (mp10) cc_final: 0.9068 (mp10) REVERT: G 354 ASN cc_start: 0.9533 (m110) cc_final: 0.9304 (m-40) REVERT: G 389 ASP cc_start: 0.9132 (m-30) cc_final: 0.8881 (m-30) REVERT: G 467 ASP cc_start: 0.7223 (t0) cc_final: 0.6985 (t0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1581 time to fit residues: 15.5972 Evaluate side-chains 73 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 0.0470 chunk 24 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 overall best weight: 2.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN F 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.071051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.057397 restraints weight = 36726.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.061083 restraints weight = 16321.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.063647 restraints weight = 9064.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.065396 restraints weight = 5653.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.066670 restraints weight = 3834.588| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3392 Z= 0.131 Angle : 0.518 5.549 4618 Z= 0.269 Chirality : 0.041 0.138 502 Planarity : 0.004 0.035 595 Dihedral : 5.224 51.034 507 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.32 % Favored : 87.44 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.37), residues: 414 helix: -2.64 (0.96), residues: 25 sheet: -0.62 (0.45), residues: 121 loop : -2.66 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 96 TYR 0.009 0.001 TYR F 86 PHE 0.010 0.001 PHE F 71 TRP 0.006 0.001 TRP F 35 HIS 0.003 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3384) covalent geometry : angle 0.51571 ( 4600) SS BOND : bond 0.00327 ( 6) SS BOND : angle 0.71396 ( 12) hydrogen bonds : bond 0.02576 ( 74) hydrogen bonds : angle 5.38714 ( 168) link_BETA1-4 : bond 0.00050 ( 1) link_BETA1-4 : angle 1.18029 ( 3) link_NAG-ASN : bond 0.00071 ( 1) link_NAG-ASN : angle 1.17136 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 100 GLN cc_start: 0.9316 (mp10) cc_final: 0.8989 (mp10) REVERT: G 389 ASP cc_start: 0.9140 (m-30) cc_final: 0.8902 (m-30) REVERT: G 452 LEU cc_start: 0.9085 (mm) cc_final: 0.8849 (mm) REVERT: G 467 ASP cc_start: 0.7246 (t0) cc_final: 0.6998 (t0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1607 time to fit residues: 16.5900 Evaluate side-chains 72 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.071410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.058027 restraints weight = 35719.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.061686 restraints weight = 15680.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.064246 restraints weight = 8679.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.066000 restraints weight = 5375.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.067225 restraints weight = 3616.504| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3392 Z= 0.100 Angle : 0.528 5.530 4618 Z= 0.273 Chirality : 0.042 0.141 502 Planarity : 0.004 0.030 595 Dihedral : 5.230 51.655 507 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.18 % Favored : 90.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.37), residues: 414 helix: -2.49 (1.01), residues: 25 sheet: -0.43 (0.45), residues: 118 loop : -2.67 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 96 TYR 0.011 0.001 TYR F 86 PHE 0.006 0.001 PHE F 71 TRP 0.010 0.001 TRP F 35 HIS 0.004 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 3384) covalent geometry : angle 0.52673 ( 4600) SS BOND : bond 0.00380 ( 6) SS BOND : angle 0.76594 ( 12) hydrogen bonds : bond 0.02602 ( 74) hydrogen bonds : angle 5.34705 ( 168) link_BETA1-4 : bond 0.00141 ( 1) link_BETA1-4 : angle 0.90283 ( 3) link_NAG-ASN : bond 0.00235 ( 1) link_NAG-ASN : angle 0.88875 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 100 GLN cc_start: 0.9323 (mp10) cc_final: 0.8997 (mp10) REVERT: G 354 ASN cc_start: 0.9563 (m-40) cc_final: 0.9356 (m-40) REVERT: G 389 ASP cc_start: 0.9153 (m-30) cc_final: 0.8920 (m-30) REVERT: G 467 ASP cc_start: 0.7273 (t0) cc_final: 0.7029 (t0) REVERT: G 492 LEU cc_start: 0.9259 (mt) cc_final: 0.8773 (mp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1475 time to fit residues: 15.1741 Evaluate side-chains 72 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.0970 chunk 32 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN F 37 GLN G 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.070733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.057248 restraints weight = 36216.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.060953 restraints weight = 15805.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.063546 restraints weight = 8690.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.065314 restraints weight = 5361.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.066582 restraints weight = 3591.051| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3392 Z= 0.118 Angle : 0.525 5.557 4618 Z= 0.272 Chirality : 0.041 0.137 502 Planarity : 0.004 0.035 595 Dihedral : 5.220 51.330 507 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.11 % Favored : 88.65 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.37), residues: 414 helix: -2.42 (0.99), residues: 25 sheet: -0.52 (0.45), residues: 120 loop : -2.70 (0.33), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 96 TYR 0.007 0.001 TYR F 36 PHE 0.008 0.001 PHE F 71 TRP 0.006 0.001 TRP F 35 HIS 0.004 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3384) covalent geometry : angle 0.52304 ( 4600) SS BOND : bond 0.00385 ( 6) SS BOND : angle 0.76728 ( 12) hydrogen bonds : bond 0.02578 ( 74) hydrogen bonds : angle 5.37139 ( 168) link_BETA1-4 : bond 0.00014 ( 1) link_BETA1-4 : angle 1.10654 ( 3) link_NAG-ASN : bond 0.00135 ( 1) link_NAG-ASN : angle 1.08745 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1491.16 seconds wall clock time: 25 minutes 59.20 seconds (1559.20 seconds total)