Starting phenix.real_space_refine on Fri Oct 10 11:58:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k11_36783/10_2025/8k11_36783.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k11_36783/10_2025/8k11_36783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k11_36783/10_2025/8k11_36783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k11_36783/10_2025/8k11_36783.map" model { file = "/net/cci-nas-00/data/ceres_data/8k11_36783/10_2025/8k11_36783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k11_36783/10_2025/8k11_36783.cif" } resolution = 3.3 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= 0.062 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 16 5.16 5 C 2794 2.51 5 N 716 2.21 5 O 876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4402 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2089 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 249} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2089 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 249} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "O" 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 Chain: "C" 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 Chain: "D" 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 Chain: "E" 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 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.16, per 1000 atoms: 0.26 Number of scatterers: 4402 At special positions: 0 Unit cell: (79.54, 74.62, 67.24, 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 16 16.00 O 876 8.00 N 716 7.00 C 2794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 256 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 301 " - " ASN A 27 " " NAG A 302 " - " ASN A 60 " " NAG A 303 " - " ASN A 123 " " NAG A 304 " - " ASN A 141 " " NAG B 301 " - " ASN B 27 " " NAG B 302 " - " ASN B 60 " " NAG B 303 " - " ASN B 123 " " NAG B 304 " - " ASN B 141 " " NAG C 1 " - " ASN B 54 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN B 165 " " NAG O 1 " - " ASN A 54 " Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 161.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.803A pdb=" N VAL A 57 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 126 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.067A pdb=" N LYS A 106 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 166 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.805A pdb=" N VAL B 57 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 126 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 43 Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.069A pdb=" N LYS B 106 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 166 Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 177 162 hydrogen bonds defined for protein. 432 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: 0.56 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1402 1.34 - 1.46: 1071 1.46 - 1.58: 1995 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 4492 Sorted by residual: bond pdb=" N ASN B 214 " pdb=" CA ASN B 214 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.33e-02 5.65e+03 7.43e+00 bond pdb=" N ASN A 214 " pdb=" CA ASN A 214 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.33e-02 5.65e+03 7.07e+00 bond pdb=" N MET B 221 " pdb=" CA MET B 221 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.23e-02 6.61e+03 5.26e+00 bond pdb=" N MET A 221 " pdb=" CA MET A 221 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.23e-02 6.61e+03 5.18e+00 bond pdb=" N ASP A 204 " pdb=" CA ASP A 204 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.34e-02 5.57e+03 4.44e+00 ... (remaining 4487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.73: 5259 0.73 - 1.45: 592 1.45 - 2.18: 178 2.18 - 2.90: 63 2.90 - 3.63: 20 Bond angle restraints: 6112 Sorted by residual: angle pdb=" CA PHE B 178 " pdb=" CB PHE B 178 " pdb=" CG PHE B 178 " ideal model delta sigma weight residual 113.80 116.91 -3.11 1.00e+00 1.00e+00 9.69e+00 angle pdb=" CA PHE A 178 " pdb=" CB PHE A 178 " pdb=" CG PHE A 178 " ideal model delta sigma weight residual 113.80 116.88 -3.08 1.00e+00 1.00e+00 9.47e+00 angle pdb=" CA ASP A 204 " pdb=" C ASP A 204 " pdb=" O ASP A 204 " ideal model delta sigma weight residual 121.87 118.78 3.09 1.16e+00 7.43e-01 7.11e+00 angle pdb=" CA ASP B 204 " pdb=" C ASP B 204 " pdb=" O ASP B 204 " ideal model delta sigma weight residual 121.87 118.87 3.00 1.16e+00 7.43e-01 6.71e+00 angle pdb=" C PHE A 178 " pdb=" CA PHE A 178 " pdb=" CB PHE A 178 " ideal model delta sigma weight residual 109.62 105.99 3.63 1.57e+00 4.06e-01 5.34e+00 ... (remaining 6107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 2481 15.74 - 31.49: 320 31.49 - 47.23: 91 47.23 - 62.97: 28 62.97 - 78.71: 6 Dihedral angle restraints: 2926 sinusoidal: 1362 harmonic: 1564 Sorted by residual: dihedral pdb=" CB CYS A 117 " pdb=" SG CYS A 117 " pdb=" SG CYS A 207 " pdb=" CB CYS A 207 " ideal model delta sinusoidal sigma weight residual -86.00 -122.47 36.47 1 1.00e+01 1.00e-02 1.88e+01 dihedral pdb=" CB CYS B 117 " pdb=" SG CYS B 117 " pdb=" SG CYS B 207 " pdb=" CB CYS B 207 " ideal model delta sinusoidal sigma weight residual -86.00 -122.47 36.47 1 1.00e+01 1.00e-02 1.88e+01 dihedral pdb=" SG CYS A 117 " pdb=" CB CYS A 207 " pdb=" SG CYS A 207 " pdb=" CA CYS A 207 " ideal model delta sinusoidal sigma weight residual 79.00 18.79 60.21 1 2.00e+01 2.50e-03 1.21e+01 ... (remaining 2923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 694 0.104 - 0.207: 48 0.207 - 0.311: 5 0.311 - 0.415: 0 0.415 - 0.519: 1 Chirality restraints: 748 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" CA PHE B 178 " pdb=" N PHE B 178 " pdb=" C PHE B 178 " pdb=" CB PHE B 178 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA PHE A 178 " pdb=" N PHE A 178 " pdb=" C PHE A 178 " pdb=" CB PHE A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 745 not shown) Planarity restraints: 786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 165 " -0.039 2.00e-02 2.50e+03 4.81e-02 2.89e+01 pdb=" CG ASN B 165 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN B 165 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 165 " 0.082 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 123 " -0.038 2.00e-02 2.50e+03 4.19e-02 2.19e+01 pdb=" CG ASN B 123 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN B 123 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 123 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG B 303 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 54 " -0.019 2.00e-02 2.50e+03 2.13e-02 5.66e+00 pdb=" CG ASN B 54 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN B 54 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 54 " 0.034 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.026 2.00e-02 2.50e+03 ... (remaining 783 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 480 2.75 - 3.29: 3887 3.29 - 3.83: 6736 3.83 - 4.36: 7686 4.36 - 4.90: 13590 Nonbonded interactions: 32379 Sorted by model distance: nonbonded pdb=" OD1 ASN A 165 " pdb=" OG1 THR A 279 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASN B 165 " pdb=" OG1 THR B 279 " model vdw 2.216 3.040 nonbonded pdb=" O LEU B 116 " pdb=" OH TYR B 173 " model vdw 2.297 3.040 nonbonded pdb=" O LEU A 116 " pdb=" OH TYR A 173 " model vdw 2.297 3.040 nonbonded pdb=" O ALA B 194 " pdb=" OG1 THR B 226 " model vdw 2.297 3.040 ... (remaining 32374 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'O' } 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: 2.790 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.390 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 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 : 0.004 0.036 4512 Z= 0.227 Angle : 0.716 17.163 6168 Z= 0.344 Chirality : 0.057 0.519 748 Planarity : 0.003 0.034 774 Dihedral : 15.604 78.712 1898 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.42 % Allowed : 23.52 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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 aren not related in a simple way. whole: 0.27 (0.36), residues: 522 helix: None (None), residues: 0 sheet: 1.68 (0.29), residues: 270 loop : -1.68 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 147 TYR 0.012 0.001 TYR A 173 PHE 0.015 0.001 PHE A 178 HIS 0.005 0.002 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 4492) covalent geometry : angle 0.59300 ( 6112) SS BOND : bond 0.00282 ( 4) SS BOND : angle 0.76991 ( 8) hydrogen bonds : bond 0.07132 ( 162) hydrogen bonds : angle 5.97429 ( 432) link_BETA1-4 : bond 0.00388 ( 4) link_BETA1-4 : angle 1.07754 ( 12) link_NAG-ASN : bond 0.00673 ( 12) link_NAG-ASN : angle 5.26205 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.6680 (mmm160) cc_final: 0.6385 (mtp180) REVERT: A 112 VAL cc_start: 0.8849 (p) cc_final: 0.8556 (m) REVERT: B 105 ARG cc_start: 0.6671 (mmm160) cc_final: 0.6376 (mtp180) REVERT: B 112 VAL cc_start: 0.8856 (p) cc_final: 0.8570 (m) outliers start: 2 outliers final: 0 residues processed: 109 average time/residue: 0.0982 time to fit residues: 12.8004 Evaluate side-chains 64 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.199454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.153023 restraints weight = 4928.977| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.08 r_work: 0.3558 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4512 Z= 0.179 Angle : 0.647 9.294 6168 Z= 0.326 Chirality : 0.051 0.202 748 Planarity : 0.004 0.022 774 Dihedral : 7.157 59.791 910 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.03 % Allowed : 22.88 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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 aren not related in a simple way. whole: 0.25 (0.36), residues: 522 helix: -4.87 (0.44), residues: 14 sheet: 1.67 (0.30), residues: 260 loop : -1.29 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 85 TYR 0.016 0.002 TYR A 173 PHE 0.012 0.002 PHE A 243 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 4492) covalent geometry : angle 0.59279 ( 6112) SS BOND : bond 0.00676 ( 4) SS BOND : angle 0.63780 ( 8) hydrogen bonds : bond 0.03555 ( 162) hydrogen bonds : angle 5.54632 ( 432) link_BETA1-4 : bond 0.00407 ( 4) link_BETA1-4 : angle 0.99103 ( 12) link_NAG-ASN : bond 0.00546 ( 12) link_NAG-ASN : angle 3.41847 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7919 (mtp-110) cc_final: 0.7549 (mtp85) REVERT: A 102 MET cc_start: 0.7572 (ttm) cc_final: 0.7212 (ttm) REVERT: A 112 VAL cc_start: 0.8893 (p) cc_final: 0.8626 (m) REVERT: B 59 ARG cc_start: 0.7914 (mtp-110) cc_final: 0.7558 (mtp85) REVERT: B 102 MET cc_start: 0.7563 (ttm) cc_final: 0.7216 (ttm) REVERT: B 112 VAL cc_start: 0.8895 (p) cc_final: 0.8607 (m) outliers start: 19 outliers final: 10 residues processed: 73 average time/residue: 0.0984 time to fit residues: 8.6702 Evaluate side-chains 60 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 283 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** 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 = 0.4276 r_free = 0.4276 target = 0.198241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150792 restraints weight = 4933.517| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.07 r_work: 0.3552 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4512 Z= 0.171 Angle : 0.603 8.659 6168 Z= 0.310 Chirality : 0.052 0.248 748 Planarity : 0.003 0.024 774 Dihedral : 6.346 54.861 910 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.03 % Allowed : 24.15 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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 aren not related in a simple way. whole: 0.30 (0.36), residues: 522 helix: -4.81 (0.47), residues: 14 sheet: 1.78 (0.30), residues: 260 loop : -1.35 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 85 TYR 0.015 0.001 TYR A 173 PHE 0.011 0.002 PHE A 130 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 4492) covalent geometry : angle 0.56135 ( 6112) SS BOND : bond 0.00310 ( 4) SS BOND : angle 1.81896 ( 8) hydrogen bonds : bond 0.03549 ( 162) hydrogen bonds : angle 5.38187 ( 432) link_BETA1-4 : bond 0.00286 ( 4) link_BETA1-4 : angle 0.95035 ( 12) link_NAG-ASN : bond 0.00817 ( 12) link_NAG-ASN : angle 2.77431 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7974 (mtp-110) cc_final: 0.7604 (mtp85) REVERT: A 228 LYS cc_start: 0.6335 (pttm) cc_final: 0.5307 (mtmt) REVERT: B 59 ARG cc_start: 0.7955 (mtp-110) cc_final: 0.7580 (mtp85) REVERT: B 228 LYS cc_start: 0.6320 (pttm) cc_final: 0.5312 (mtmt) outliers start: 19 outliers final: 12 residues processed: 65 average time/residue: 0.0889 time to fit residues: 7.1196 Evaluate side-chains 55 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 283 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** 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 = 0.4273 r_free = 0.4273 target = 0.197284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149548 restraints weight = 4895.536| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.17 r_work: 0.3545 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4512 Z= 0.150 Angle : 0.577 8.205 6168 Z= 0.290 Chirality : 0.050 0.212 748 Planarity : 0.003 0.021 774 Dihedral : 5.314 42.200 910 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.45 % Allowed : 23.09 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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 aren not related in a simple way. whole: 0.27 (0.36), residues: 522 helix: -4.75 (0.50), residues: 14 sheet: 1.76 (0.30), residues: 260 loop : -1.40 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 85 TYR 0.015 0.001 TYR A 173 PHE 0.012 0.002 PHE A 130 HIS 0.003 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4492) covalent geometry : angle 0.54199 ( 6112) SS BOND : bond 0.00369 ( 4) SS BOND : angle 1.37864 ( 8) hydrogen bonds : bond 0.03351 ( 162) hydrogen bonds : angle 5.34833 ( 432) link_BETA1-4 : bond 0.00354 ( 4) link_BETA1-4 : angle 0.82819 ( 12) link_NAG-ASN : bond 0.00627 ( 12) link_NAG-ASN : angle 2.55160 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.195 Fit side-chains REVERT: A 59 ARG cc_start: 0.7977 (mtp-110) cc_final: 0.7601 (mtp85) REVERT: A 228 LYS cc_start: 0.6188 (pttm) cc_final: 0.5100 (mtmt) REVERT: B 59 ARG cc_start: 0.7955 (mtp-110) cc_final: 0.7598 (mtp85) REVERT: B 228 LYS cc_start: 0.6165 (pttm) cc_final: 0.5105 (mtmt) outliers start: 21 outliers final: 14 residues processed: 54 average time/residue: 0.0828 time to fit residues: 5.6753 Evaluate side-chains 48 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 283 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.0020 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** 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 = 0.4282 r_free = 0.4282 target = 0.198774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150973 restraints weight = 4864.386| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.07 r_work: 0.3567 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4512 Z= 0.122 Angle : 0.537 7.862 6168 Z= 0.275 Chirality : 0.049 0.175 748 Planarity : 0.003 0.021 774 Dihedral : 4.848 34.794 910 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.75 % Allowed : 24.58 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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 aren not related in a simple way. whole: 0.31 (0.36), residues: 522 helix: None (None), residues: 0 sheet: 1.68 (0.30), residues: 260 loop : -1.48 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 85 TYR 0.013 0.001 TYR A 173 PHE 0.012 0.001 PHE A 130 HIS 0.003 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4492) covalent geometry : angle 0.50444 ( 6112) SS BOND : bond 0.00124 ( 4) SS BOND : angle 0.81200 ( 8) hydrogen bonds : bond 0.03191 ( 162) hydrogen bonds : angle 5.24164 ( 432) link_BETA1-4 : bond 0.00341 ( 4) link_BETA1-4 : angle 0.84159 ( 12) link_NAG-ASN : bond 0.00515 ( 12) link_NAG-ASN : angle 2.41618 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7891 (mtp-110) cc_final: 0.7521 (mtp85) REVERT: A 228 LYS cc_start: 0.6176 (pttm) cc_final: 0.5058 (mtmt) REVERT: B 59 ARG cc_start: 0.7917 (mtp-110) cc_final: 0.7583 (mtp85) REVERT: B 228 LYS cc_start: 0.6148 (pttm) cc_final: 0.5061 (mtmt) outliers start: 13 outliers final: 13 residues processed: 54 average time/residue: 0.0653 time to fit residues: 4.6322 Evaluate side-chains 55 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 283 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 0.0970 chunk 5 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** 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 = 0.4294 r_free = 0.4294 target = 0.200482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.152249 restraints weight = 4967.880| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.13 r_work: 0.3564 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 4512 Z= 0.104 Angle : 0.539 7.575 6168 Z= 0.271 Chirality : 0.049 0.192 748 Planarity : 0.003 0.022 774 Dihedral : 4.568 34.311 910 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.97 % Allowed : 25.64 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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 aren not related in a simple way. whole: 0.25 (0.36), residues: 522 helix: -4.66 (0.53), residues: 14 sheet: 1.64 (0.30), residues: 260 loop : -1.26 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 85 TYR 0.012 0.001 TYR A 173 PHE 0.013 0.001 PHE A 130 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 4492) covalent geometry : angle 0.49592 ( 6112) SS BOND : bond 0.00341 ( 4) SS BOND : angle 1.46412 ( 8) hydrogen bonds : bond 0.03010 ( 162) hydrogen bonds : angle 5.12145 ( 432) link_BETA1-4 : bond 0.00434 ( 4) link_BETA1-4 : angle 0.82486 ( 12) link_NAG-ASN : bond 0.00510 ( 12) link_NAG-ASN : angle 2.69574 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7919 (mtp-110) cc_final: 0.7550 (mtp85) REVERT: A 228 LYS cc_start: 0.6158 (pttm) cc_final: 0.5011 (mtmt) REVERT: B 59 ARG cc_start: 0.7955 (mtp-110) cc_final: 0.7619 (mtp85) REVERT: B 228 LYS cc_start: 0.6151 (pttm) cc_final: 0.5024 (mtmt) outliers start: 14 outliers final: 13 residues processed: 56 average time/residue: 0.0881 time to fit residues: 6.1924 Evaluate side-chains 56 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 283 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** 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 = 0.4262 r_free = 0.4262 target = 0.195872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148934 restraints weight = 4850.456| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.04 r_work: 0.3553 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 4512 Z= 0.126 Angle : 0.538 7.434 6168 Z= 0.272 Chirality : 0.050 0.235 748 Planarity : 0.003 0.022 774 Dihedral : 4.433 31.348 910 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.03 % Allowed : 23.31 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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 aren not related in a simple way. whole: 0.35 (0.35), residues: 522 helix: None (None), residues: 0 sheet: 1.58 (0.29), residues: 260 loop : -1.29 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 85 TYR 0.014 0.001 TYR A 173 PHE 0.016 0.001 PHE A 82 HIS 0.003 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4492) covalent geometry : angle 0.50284 ( 6112) SS BOND : bond 0.00147 ( 4) SS BOND : angle 0.79623 ( 8) hydrogen bonds : bond 0.03203 ( 162) hydrogen bonds : angle 5.12649 ( 432) link_BETA1-4 : bond 0.00319 ( 4) link_BETA1-4 : angle 0.85425 ( 12) link_NAG-ASN : bond 0.00531 ( 12) link_NAG-ASN : angle 2.49731 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7963 (mtp-110) cc_final: 0.7619 (mtp85) REVERT: A 228 LYS cc_start: 0.6373 (pttm) cc_final: 0.5078 (mtmt) REVERT: B 59 ARG cc_start: 0.7881 (mtp-110) cc_final: 0.7558 (mtp85) REVERT: B 228 LYS cc_start: 0.6349 (pttm) cc_final: 0.5098 (mtmt) outliers start: 19 outliers final: 17 residues processed: 59 average time/residue: 0.0952 time to fit residues: 7.0391 Evaluate side-chains 57 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 283 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.192588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.143952 restraints weight = 4907.092| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.17 r_work: 0.3510 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 4512 Z= 0.268 Angle : 0.679 7.605 6168 Z= 0.347 Chirality : 0.054 0.215 748 Planarity : 0.004 0.028 774 Dihedral : 4.955 31.842 910 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.03 % Allowed : 24.15 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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 aren not related in a simple way. whole: 0.16 (0.36), residues: 522 helix: None (None), residues: 0 sheet: 1.35 (0.30), residues: 264 loop : -1.34 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 85 TYR 0.022 0.002 TYR A 173 PHE 0.017 0.002 PHE A 35 HIS 0.003 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00660 ( 4492) covalent geometry : angle 0.64433 ( 6112) SS BOND : bond 0.00268 ( 4) SS BOND : angle 2.32199 ( 8) hydrogen bonds : bond 0.04048 ( 162) hydrogen bonds : angle 5.54483 ( 432) link_BETA1-4 : bond 0.00264 ( 4) link_BETA1-4 : angle 0.80284 ( 12) link_NAG-ASN : bond 0.00488 ( 12) link_NAG-ASN : angle 2.68488 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7600 (mtp85) REVERT: A 228 LYS cc_start: 0.6313 (pttm) cc_final: 0.4869 (mmtt) REVERT: B 59 ARG cc_start: 0.7910 (mtp-110) cc_final: 0.7568 (mtp85) REVERT: B 228 LYS cc_start: 0.6320 (pttm) cc_final: 0.4847 (mmtt) outliers start: 19 outliers final: 19 residues processed: 58 average time/residue: 0.0856 time to fit residues: 6.2630 Evaluate side-chains 52 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 33 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 283 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.198515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.149956 restraints weight = 4941.930| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.13 r_work: 0.3517 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 4512 Z= 0.120 Angle : 0.566 6.831 6168 Z= 0.287 Chirality : 0.051 0.226 748 Planarity : 0.003 0.026 774 Dihedral : 4.635 30.924 910 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.39 % Allowed : 25.21 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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 aren not related in a simple way. whole: 0.30 (0.36), residues: 522 helix: None (None), residues: 0 sheet: 1.45 (0.30), residues: 260 loop : -1.20 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.013 0.001 TYR A 173 PHE 0.014 0.001 PHE A 130 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4492) covalent geometry : angle 0.52364 ( 6112) SS BOND : bond 0.00328 ( 4) SS BOND : angle 2.05877 ( 8) hydrogen bonds : bond 0.03317 ( 162) hydrogen bonds : angle 5.26411 ( 432) link_BETA1-4 : bond 0.00312 ( 4) link_BETA1-4 : angle 0.77333 ( 12) link_NAG-ASN : bond 0.00463 ( 12) link_NAG-ASN : angle 2.68421 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.169 Fit side-chains REVERT: A 228 LYS cc_start: 0.6388 (pttm) cc_final: 0.5119 (mmtt) REVERT: B 228 LYS cc_start: 0.6386 (pttm) cc_final: 0.5124 (mmtt) outliers start: 16 outliers final: 13 residues processed: 45 average time/residue: 0.0683 time to fit residues: 4.0655 Evaluate side-chains 44 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 283 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 35 optimal weight: 0.0000 chunk 1 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** 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 = 0.4261 r_free = 0.4261 target = 0.196332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149688 restraints weight = 4830.094| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 3.08 r_work: 0.3559 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 4512 Z= 0.111 Angle : 0.544 6.547 6168 Z= 0.275 Chirality : 0.049 0.191 748 Planarity : 0.003 0.024 774 Dihedral : 4.508 35.622 910 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.75 % Allowed : 25.21 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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 aren not related in a simple way. whole: 0.37 (0.36), residues: 522 helix: None (None), residues: 0 sheet: 1.45 (0.30), residues: 260 loop : -1.11 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 100 TYR 0.012 0.001 TYR A 173 PHE 0.013 0.001 PHE A 130 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 4492) covalent geometry : angle 0.50833 ( 6112) SS BOND : bond 0.00273 ( 4) SS BOND : angle 1.76960 ( 8) hydrogen bonds : bond 0.03083 ( 162) hydrogen bonds : angle 5.12052 ( 432) link_BETA1-4 : bond 0.00322 ( 4) link_BETA1-4 : angle 0.83585 ( 12) link_NAG-ASN : bond 0.00472 ( 12) link_NAG-ASN : angle 2.41459 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.174 Fit side-chains REVERT: A 228 LYS cc_start: 0.6422 (pttm) cc_final: 0.5155 (mmtt) REVERT: B 228 LYS cc_start: 0.6328 (pttm) cc_final: 0.5134 (mmtt) outliers start: 13 outliers final: 12 residues processed: 46 average time/residue: 0.0787 time to fit residues: 4.7427 Evaluate side-chains 46 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 283 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.0270 chunk 7 optimal weight: 0.0470 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.197547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151033 restraints weight = 4897.744| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.08 r_work: 0.3578 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 4512 Z= 0.096 Angle : 0.526 6.274 6168 Z= 0.265 Chirality : 0.049 0.198 748 Planarity : 0.003 0.030 774 Dihedral : 4.383 38.442 910 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.39 % Allowed : 24.79 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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 aren not related in a simple way. whole: 0.41 (0.36), residues: 522 helix: None (None), residues: 0 sheet: 1.47 (0.30), residues: 260 loop : -1.06 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.011 0.001 TYR A 173 PHE 0.014 0.001 PHE A 130 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 4492) covalent geometry : angle 0.49316 ( 6112) SS BOND : bond 0.00266 ( 4) SS BOND : angle 1.54203 ( 8) hydrogen bonds : bond 0.02958 ( 162) hydrogen bonds : angle 5.01249 ( 432) link_BETA1-4 : bond 0.00333 ( 4) link_BETA1-4 : angle 0.88904 ( 12) link_NAG-ASN : bond 0.00471 ( 12) link_NAG-ASN : angle 2.28965 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1183.94 seconds wall clock time: 21 minutes 1.56 seconds (1261.56 seconds total)