Starting phenix.real_space_refine on Sun Apr 27 04:05:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k11_36783/04_2025/8k11_36783.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k11_36783/04_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_36783/04_2025/8k11_36783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k11_36783/04_2025/8k11_36783.map" model { file = "/net/cci-nas-00/data/ceres_data/8k11_36783/04_2025/8k11_36783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k11_36783/04_2025/8k11_36783.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 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: 3.78, per 1000 atoms: 0.86 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: 1.15 Conformation dependent library (CDL) restraints added in 495.6 milliseconds 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: 0.54 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: 1.12 Time building geometry restraints manager: 1.34 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: 0.02 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: 2.590 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.040 Find NCS groups from input model: 0.140 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.740 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.005 0.002 HIS A 55 PHE 0.015 0.001 PHE A 178 TYR 0.012 0.001 TYR A 173 ARG 0.003 0.000 ARG A 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 12) link_NAG-ASN : angle 5.26205 ( 36) link_BETA1-4 : bond 0.00388 ( 4) link_BETA1-4 : angle 1.07754 ( 12) hydrogen bonds : bond 0.07132 ( 162) hydrogen bonds : angle 5.97429 ( 432) SS BOND : bond 0.00282 ( 4) SS BOND : angle 0.76991 ( 8) covalent geometry : bond 0.00433 ( 4492) covalent geometry : angle 0.59300 ( 6112) *********************** 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 : 0.440 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: 0.2187 time to fit residues: 28.4765 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 : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 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** 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 = 0.4319 r_free = 0.4319 target = 0.203431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158345 restraints weight = 4910.329| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.03 r_work: 0.3625 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4512 Z= 0.117 Angle : 0.596 9.277 6168 Z= 0.298 Chirality : 0.049 0.205 748 Planarity : 0.003 0.023 774 Dihedral : 7.093 58.589 910 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.81 % Allowed : 22.88 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.35), residues: 522 helix: None (None), residues: 0 sheet: 1.91 (0.29), residues: 250 loop : -1.38 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 55 PHE 0.011 0.001 PHE A 243 TYR 0.014 0.001 TYR A 176 ARG 0.003 0.001 ARG A 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 12) link_NAG-ASN : angle 3.37060 ( 36) link_BETA1-4 : bond 0.00416 ( 4) link_BETA1-4 : angle 1.04008 ( 12) hydrogen bonds : bond 0.03246 ( 162) hydrogen bonds : angle 5.40338 ( 432) SS BOND : bond 0.00693 ( 4) SS BOND : angle 1.09664 ( 8) covalent geometry : bond 0.00264 ( 4492) covalent geometry : angle 0.53663 ( 6112) *********************** 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 77 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7933 (mtp-110) cc_final: 0.7560 (mtp85) REVERT: A 102 MET cc_start: 0.7513 (ttm) cc_final: 0.7176 (ttm) REVERT: A 112 VAL cc_start: 0.8842 (p) cc_final: 0.8606 (m) REVERT: A 188 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8634 (mtmm) REVERT: B 59 ARG cc_start: 0.7926 (mtp-110) cc_final: 0.7565 (mtp85) REVERT: B 102 MET cc_start: 0.7455 (ttm) cc_final: 0.7128 (ttm) REVERT: B 112 VAL cc_start: 0.8861 (p) cc_final: 0.8594 (m) REVERT: B 188 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8595 (mtmm) outliers start: 18 outliers final: 8 residues processed: 71 average time/residue: 0.2787 time to fit residues: 24.2764 Evaluate side-chains 61 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 188 LYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 221 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.201795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.155030 restraints weight = 4922.307| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.08 r_work: 0.3587 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4512 Z= 0.123 Angle : 0.562 8.545 6168 Z= 0.286 Chirality : 0.049 0.246 748 Planarity : 0.003 0.023 774 Dihedral : 6.230 56.312 910 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.81 % Allowed : 23.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.36), residues: 522 helix: -4.92 (0.40), residues: 14 sheet: 1.69 (0.30), residues: 262 loop : -1.22 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 55 PHE 0.011 0.001 PHE B 130 TYR 0.011 0.001 TYR B 173 ARG 0.005 0.000 ARG A 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 12) link_NAG-ASN : angle 2.71332 ( 36) link_BETA1-4 : bond 0.00366 ( 4) link_BETA1-4 : angle 1.07821 ( 12) hydrogen bonds : bond 0.03275 ( 162) hydrogen bonds : angle 5.35473 ( 432) SS BOND : bond 0.00122 ( 4) SS BOND : angle 1.53182 ( 8) covalent geometry : bond 0.00279 ( 4492) covalent geometry : angle 0.51934 ( 6112) *********************** 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: 18 poor density : 51 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7962 (mtp-110) cc_final: 0.7578 (mtp85) REVERT: A 102 MET cc_start: 0.7326 (ttm) cc_final: 0.6989 (ttm) REVERT: A 112 VAL cc_start: 0.8835 (p) cc_final: 0.8578 (m) REVERT: B 59 ARG cc_start: 0.7957 (mtp-110) cc_final: 0.7581 (mtp85) REVERT: B 112 VAL cc_start: 0.8812 (p) cc_final: 0.8561 (m) outliers start: 18 outliers final: 12 residues processed: 64 average time/residue: 0.2183 time to fit residues: 17.0125 Evaluate side-chains 59 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.198581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.150926 restraints weight = 4901.182| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.10 r_work: 0.3549 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2967 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= 0.164 Angle : 0.588 8.286 6168 Z= 0.302 Chirality : 0.051 0.211 748 Planarity : 0.003 0.020 774 Dihedral : 5.386 45.711 910 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.03 % Allowed : 22.67 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.36), residues: 522 helix: -4.86 (0.43), residues: 14 sheet: 1.65 (0.30), residues: 262 loop : -1.22 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 55 PHE 0.010 0.002 PHE A 195 TYR 0.013 0.001 TYR B 173 ARG 0.005 0.001 ARG B 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 12) link_NAG-ASN : angle 2.55458 ( 36) link_BETA1-4 : bond 0.00357 ( 4) link_BETA1-4 : angle 0.87080 ( 12) hydrogen bonds : bond 0.03489 ( 162) hydrogen bonds : angle 5.30002 ( 432) SS BOND : bond 0.00268 ( 4) SS BOND : angle 2.15078 ( 8) covalent geometry : bond 0.00392 ( 4492) covalent geometry : angle 0.55047 ( 6112) *********************** 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 75 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.591 Fit side-chains REVERT: A 59 ARG cc_start: 0.7988 (mtp-110) cc_final: 0.7615 (mtp85) REVERT: A 228 LYS cc_start: 0.6329 (pttm) cc_final: 0.5227 (mtmt) REVERT: B 59 ARG cc_start: 0.7982 (mtp-110) cc_final: 0.7640 (mtp85) REVERT: B 228 LYS cc_start: 0.6305 (pttm) cc_final: 0.5245 (mtmt) outliers start: 19 outliers final: 12 residues processed: 71 average time/residue: 0.2409 time to fit residues: 21.1412 Evaluate side-chains 64 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.197647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.148873 restraints weight = 4954.753| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.15 r_work: 0.3507 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 4512 Z= 0.200 Angle : 0.631 7.968 6168 Z= 0.319 Chirality : 0.052 0.199 748 Planarity : 0.004 0.026 774 Dihedral : 5.212 37.933 910 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.97 % Allowed : 24.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.36), residues: 522 helix: None (None), residues: 0 sheet: 1.58 (0.30), residues: 260 loop : -1.52 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 55 PHE 0.013 0.002 PHE B 35 TYR 0.016 0.001 TYR B 173 ARG 0.005 0.001 ARG A 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 12) link_NAG-ASN : angle 2.87376 ( 36) link_BETA1-4 : bond 0.00545 ( 4) link_BETA1-4 : angle 0.66466 ( 12) hydrogen bonds : bond 0.03679 ( 162) hydrogen bonds : angle 5.41588 ( 432) SS BOND : bond 0.00224 ( 4) SS BOND : angle 1.24858 ( 8) covalent geometry : bond 0.00483 ( 4492) covalent geometry : angle 0.59189 ( 6112) *********************** 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 61 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7894 (mtp-110) cc_final: 0.7488 (mtp85) REVERT: A 228 LYS cc_start: 0.6315 (pttm) cc_final: 0.5043 (mtmt) REVERT: B 59 ARG cc_start: 0.7896 (mtp-110) cc_final: 0.7521 (mtp85) REVERT: B 228 LYS cc_start: 0.6282 (pttm) cc_final: 0.5042 (mtmt) outliers start: 14 outliers final: 14 residues processed: 56 average time/residue: 0.2776 time to fit residues: 20.9706 Evaluate side-chains 57 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4274 r_free = 0.4274 target = 0.198459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150350 restraints weight = 4875.556| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 3.12 r_work: 0.3550 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3529 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= 0.138 Angle : 0.571 7.596 6168 Z= 0.287 Chirality : 0.050 0.186 748 Planarity : 0.003 0.024 774 Dihedral : 4.733 34.030 910 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.60 % Allowed : 23.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.36), residues: 522 helix: None (None), residues: 0 sheet: 1.53 (0.30), residues: 260 loop : -1.51 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 55 PHE 0.013 0.001 PHE B 130 TYR 0.011 0.001 TYR B 173 ARG 0.004 0.000 ARG B 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 12) link_NAG-ASN : angle 2.47850 ( 36) link_BETA1-4 : bond 0.00313 ( 4) link_BETA1-4 : angle 0.82410 ( 12) hydrogen bonds : bond 0.03357 ( 162) hydrogen bonds : angle 5.30326 ( 432) SS BOND : bond 0.00808 ( 4) SS BOND : angle 2.23002 ( 8) covalent geometry : bond 0.00321 ( 4492) covalent geometry : angle 0.53361 ( 6112) *********************** 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 53 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.483 Fit side-chains REVERT: A 59 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.7579 (mtp85) REVERT: A 228 LYS cc_start: 0.6333 (pttm) cc_final: 0.5178 (mtmt) REVERT: B 59 ARG cc_start: 0.7929 (mtp-110) cc_final: 0.7578 (mtp85) REVERT: B 228 LYS cc_start: 0.6356 (pttm) cc_final: 0.5217 (mtmt) outliers start: 17 outliers final: 13 residues processed: 51 average time/residue: 0.1724 time to fit residues: 11.3627 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 : 0.494 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.195127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148631 restraints weight = 4759.456| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.04 r_work: 0.3577 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3675 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= 0.124 Angle : 0.543 7.239 6168 Z= 0.273 Chirality : 0.049 0.176 748 Planarity : 0.003 0.023 774 Dihedral : 4.464 33.203 910 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.60 % Allowed : 23.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.36), residues: 522 helix: None (None), residues: 0 sheet: 1.50 (0.30), residues: 260 loop : -1.33 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 55 PHE 0.013 0.001 PHE A 130 TYR 0.012 0.001 TYR B 173 ARG 0.003 0.000 ARG A 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 12) link_NAG-ASN : angle 2.34750 ( 36) link_BETA1-4 : bond 0.00340 ( 4) link_BETA1-4 : angle 0.83631 ( 12) hydrogen bonds : bond 0.03178 ( 162) hydrogen bonds : angle 5.21098 ( 432) SS BOND : bond 0.00318 ( 4) SS BOND : angle 1.51802 ( 8) covalent geometry : bond 0.00289 ( 4492) covalent geometry : angle 0.51080 ( 6112) *********************** 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 59 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.7588 (mtp85) REVERT: A 228 LYS cc_start: 0.6162 (pttm) cc_final: 0.4979 (mtmt) REVERT: B 59 ARG cc_start: 0.7907 (mtp-110) cc_final: 0.7569 (mtp85) REVERT: B 228 LYS cc_start: 0.6189 (pttm) cc_final: 0.5011 (mtmt) outliers start: 17 outliers final: 17 residues processed: 56 average time/residue: 0.2113 time to fit residues: 15.8409 Evaluate side-chains 54 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 167 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 135 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 167 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.198801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.151071 restraints weight = 4857.245| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.08 r_work: 0.3562 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3786 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= 0.119 Angle : 0.549 6.994 6168 Z= 0.276 Chirality : 0.049 0.175 748 Planarity : 0.003 0.024 774 Dihedral : 4.470 31.997 910 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.18 % Allowed : 24.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.36), residues: 522 helix: None (None), residues: 0 sheet: 1.51 (0.30), residues: 260 loop : -1.23 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 55 PHE 0.013 0.001 PHE A 130 TYR 0.011 0.001 TYR A 173 ARG 0.003 0.000 ARG B 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 12) link_NAG-ASN : angle 2.57957 ( 36) link_BETA1-4 : bond 0.00323 ( 4) link_BETA1-4 : angle 0.84737 ( 12) hydrogen bonds : bond 0.03146 ( 162) hydrogen bonds : angle 5.12498 ( 432) SS BOND : bond 0.00426 ( 4) SS BOND : angle 2.11381 ( 8) covalent geometry : bond 0.00274 ( 4492) covalent geometry : angle 0.50801 ( 6112) *********************** 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 49 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.500 Fit side-chains REVERT: A 59 ARG cc_start: 0.7956 (mtp-110) cc_final: 0.7644 (mtp85) REVERT: A 228 LYS cc_start: 0.6302 (pttm) cc_final: 0.5126 (mmtt) REVERT: B 59 ARG cc_start: 0.7935 (mtp-110) cc_final: 0.7605 (mtp85) REVERT: B 228 LYS cc_start: 0.6312 (pttm) cc_final: 0.5164 (mtmt) outliers start: 15 outliers final: 15 residues processed: 46 average time/residue: 0.1777 time to fit residues: 10.8343 Evaluate side-chains 48 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 18 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.193906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.147318 restraints weight = 4818.609| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 3.05 r_work: 0.3562 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 4512 Z= 0.148 Angle : 0.568 6.813 6168 Z= 0.287 Chirality : 0.050 0.186 748 Planarity : 0.003 0.025 774 Dihedral : 4.535 35.621 910 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.81 % Allowed : 24.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.36), residues: 522 helix: None (None), residues: 0 sheet: 1.48 (0.30), residues: 260 loop : -1.20 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 55 PHE 0.011 0.002 PHE A 130 TYR 0.014 0.001 TYR A 173 ARG 0.004 0.000 ARG A 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 12) link_NAG-ASN : angle 2.48275 ( 36) link_BETA1-4 : bond 0.00298 ( 4) link_BETA1-4 : angle 0.82205 ( 12) hydrogen bonds : bond 0.03314 ( 162) hydrogen bonds : angle 5.17535 ( 432) SS BOND : bond 0.00384 ( 4) SS BOND : angle 2.15721 ( 8) covalent geometry : bond 0.00353 ( 4492) covalent geometry : angle 0.53051 ( 6112) *********************** 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 53 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 35 time to evaluate : 0.466 Fit side-chains REVERT: A 59 ARG cc_start: 0.7962 (mtp-110) cc_final: 0.7638 (mtp85) REVERT: A 228 LYS cc_start: 0.6203 (pttm) cc_final: 0.4929 (mmtt) REVERT: B 59 ARG cc_start: 0.7937 (mtp-110) cc_final: 0.7594 (mtp85) REVERT: B 228 LYS cc_start: 0.6194 (pttm) cc_final: 0.4936 (mmtt) outliers start: 18 outliers final: 17 residues processed: 49 average time/residue: 0.1564 time to fit residues: 10.0998 Evaluate side-chains 50 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 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 135 SER Chi-restraints excluded: chain B residue 136 THR 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 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 3 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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** B 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.196758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148946 restraints weight = 4862.125| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.06 r_work: 0.3537 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4512 Z= 0.166 Angle : 0.591 7.325 6168 Z= 0.297 Chirality : 0.050 0.187 748 Planarity : 0.003 0.026 774 Dihedral : 4.627 37.733 910 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.60 % Allowed : 24.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.36), residues: 522 helix: None (None), residues: 0 sheet: 1.47 (0.30), residues: 260 loop : -1.20 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 55 PHE 0.011 0.002 PHE A 130 TYR 0.014 0.001 TYR A 173 ARG 0.004 0.000 ARG A 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 12) link_NAG-ASN : angle 2.43823 ( 36) link_BETA1-4 : bond 0.00299 ( 4) link_BETA1-4 : angle 0.79386 ( 12) hydrogen bonds : bond 0.03493 ( 162) hydrogen bonds : angle 5.22210 ( 432) SS BOND : bond 0.00368 ( 4) SS BOND : angle 2.46603 ( 8) covalent geometry : bond 0.00399 ( 4492) covalent geometry : angle 0.55514 ( 6112) ********************** 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 51 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.450 Fit side-chains REVERT: A 59 ARG cc_start: 0.7972 (mtp-110) cc_final: 0.7697 (mtp85) REVERT: A 228 LYS cc_start: 0.6416 (pttm) cc_final: 0.5092 (mmtt) REVERT: B 59 ARG cc_start: 0.7951 (mtp-110) cc_final: 0.7628 (mtp85) REVERT: B 228 LYS cc_start: 0.6430 (pttm) cc_final: 0.5102 (mmtt) outliers start: 17 outliers final: 16 residues processed: 47 average time/residue: 0.1615 time to fit residues: 9.9654 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 : 0.522 ------------------------------------------------------------------------------- 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 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 135 SER Chi-restraints excluded: chain B residue 136 THR 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 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 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.195104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149013 restraints weight = 4787.832| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.01 r_work: 0.3546 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4072 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= 0.117 Angle : 0.547 6.367 6168 Z= 0.276 Chirality : 0.049 0.204 748 Planarity : 0.003 0.024 774 Dihedral : 4.438 38.442 910 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.97 % Allowed : 25.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.36), residues: 522 helix: None (None), residues: 0 sheet: 1.51 (0.30), residues: 260 loop : -1.15 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 55 PHE 0.014 0.001 PHE B 82 TYR 0.011 0.001 TYR A 173 ARG 0.003 0.000 ARG B 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 12) link_NAG-ASN : angle 2.32730 ( 36) link_BETA1-4 : bond 0.00307 ( 4) link_BETA1-4 : angle 0.80381 ( 12) hydrogen bonds : bond 0.03200 ( 162) hydrogen bonds : angle 5.15307 ( 432) SS BOND : bond 0.00288 ( 4) SS BOND : angle 1.99550 ( 8) covalent geometry : bond 0.00270 ( 4492) covalent geometry : angle 0.51381 ( 6112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2672.38 seconds wall clock time: 48 minutes 38.61 seconds (2918.61 seconds total)