Starting phenix.real_space_refine on Wed Jul 23 09:44:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lxx_23578/07_2025/7lxx_23578.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lxx_23578/07_2025/7lxx_23578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lxx_23578/07_2025/7lxx_23578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lxx_23578/07_2025/7lxx_23578.map" model { file = "/net/cci-nas-00/data/ceres_data/7lxx_23578/07_2025/7lxx_23578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lxx_23578/07_2025/7lxx_23578.cif" } resolution = 3.0 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= 0.029 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 10 5.16 5 C 1724 2.51 5 N 466 2.21 5 O 540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2740 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 971 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 777 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain breaks: 5 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.77, per 1000 atoms: 1.38 Number of scatterers: 2740 At special positions: 0 Unit cell: (71.4, 86.1, 71.4, 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 10 16.00 O 540 8.00 N 466 7.00 C 1724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.07 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 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 B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 149 " " NAG B 1 " - " ASN A 17 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 353.4 milliseconds 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 642 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 9 sheets defined 4.3% alpha, 50.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.847A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.669A pdb=" N TYR H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.530A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA8, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.464A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 83 through 84 removed outlier: 12.962A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.148A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 276 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: 0.78 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 719 1.33 - 1.45: 607 1.45 - 1.57: 1465 1.57 - 1.69: 0 1.69 - 1.81: 13 Bond restraints: 2804 Sorted by residual: bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.464 -0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.463 -0.050 2.00e-02 2.50e+03 6.20e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.461 -0.048 2.00e-02 2.50e+03 5.70e+00 bond pdb=" CD GLU A 154 " pdb=" OE2 GLU A 154 " ideal model delta sigma weight residual 1.249 1.204 0.045 1.90e-02 2.77e+03 5.54e+00 bond pdb=" CG ASP H 114 " pdb=" OD2 ASP H 114 " ideal model delta sigma weight residual 1.249 1.204 0.045 1.90e-02 2.77e+03 5.51e+00 ... (remaining 2799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 3138 1.40 - 2.81: 545 2.81 - 4.21: 89 4.21 - 5.62: 26 5.62 - 7.02: 12 Bond angle restraints: 3810 Sorted by residual: angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.05 -7.02 9.90e-01 1.02e+00 5.03e+01 angle pdb=" C ALA L 45 " pdb=" N PRO L 46 " pdb=" CA PRO L 46 " ideal model delta sigma weight residual 119.85 126.55 -6.70 1.01e+00 9.80e-01 4.40e+01 angle pdb=" C ARG L 56 " pdb=" N PRO L 57 " pdb=" CA PRO L 57 " ideal model delta sigma weight residual 119.78 126.60 -6.82 1.03e+00 9.43e-01 4.38e+01 angle pdb=" C ASP A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta sigma weight residual 120.14 126.93 -6.79 1.06e+00 8.90e-01 4.10e+01 angle pdb=" C THR A 250 " pdb=" N PRO A 251 " pdb=" CA PRO A 251 " ideal model delta sigma weight residual 119.85 126.28 -6.43 1.01e+00 9.80e-01 4.05e+01 ... (remaining 3805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 1585 14.98 - 29.95: 61 29.95 - 44.93: 11 44.93 - 59.90: 5 59.90 - 74.87: 4 Dihedral angle restraints: 1666 sinusoidal: 660 harmonic: 1006 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 120.22 -27.22 1 1.00e+01 1.00e-02 1.06e+01 dihedral pdb=" CG ARG H 67 " pdb=" CD ARG H 67 " pdb=" NE ARG H 67 " pdb=" CZ ARG H 67 " ideal model delta sinusoidal sigma weight residual 180.00 141.04 38.96 2 1.50e+01 4.44e-03 8.43e+00 dihedral pdb=" CB GLU A 154 " pdb=" CG GLU A 154 " pdb=" CD GLU A 154 " pdb=" OE1 GLU A 154 " ideal model delta sinusoidal sigma weight residual 0.00 74.87 -74.87 1 3.00e+01 1.11e-03 7.88e+00 ... (remaining 1663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 309 0.061 - 0.121: 95 0.121 - 0.181: 14 0.181 - 0.241: 7 0.241 - 0.302: 2 Chirality restraints: 427 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.72e+01 chirality pdb=" C1 FUC B 3 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 3 " pdb=" O5 FUC B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.06e+01 chirality pdb=" C2 NAG A1301 " pdb=" C1 NAG A1301 " pdb=" C3 NAG A1301 " pdb=" N2 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.79 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 424 not shown) Planarity restraints: 481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.353 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG B 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 95 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C TYR H 95 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR H 95 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS H 96 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 29 " 0.025 2.00e-02 2.50e+03 1.52e-02 4.05e+00 pdb=" CG PHE H 29 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE H 29 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE H 29 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE H 29 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 29 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE H 29 " 0.014 2.00e-02 2.50e+03 ... (remaining 478 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 1519 3.00 - 3.47: 2371 3.47 - 3.95: 4484 3.95 - 4.42: 5187 4.42 - 4.90: 8533 Nonbonded interactions: 22094 Sorted by model distance: nonbonded pdb=" OD2 ASP H 73 " pdb=" NZ LYS H 76 " model vdw 2.519 3.120 nonbonded pdb=" N ASP H 62 " pdb=" OD1 ASP H 62 " model vdw 2.529 3.120 nonbonded pdb=" O THR A 250 " pdb=" OG1 THR A 250 " model vdw 2.573 3.040 nonbonded pdb=" N ASN L 33 " pdb=" OD1 ASN L 33 " model vdw 2.579 3.120 nonbonded pdb=" N LYS H 104 " pdb=" N TRP H 105 " model vdw 2.582 2.560 ... (remaining 22089 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.180 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.070 Find NCS groups from input model: 0.040 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:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 : 0.012 0.056 2811 Z= 0.665 Angle : 1.200 7.023 3828 Z= 0.796 Chirality : 0.064 0.302 427 Planarity : 0.015 0.306 479 Dihedral : 9.984 74.874 1015 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.72 (0.40), residues: 154 loop : 0.35 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP L 101 HIS 0.002 0.001 HIS A 66 PHE 0.025 0.004 PHE H 29 TYR 0.025 0.004 TYR H 103 ARG 0.004 0.001 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.05294 ( 2) link_NAG-ASN : angle 2.28691 ( 6) link_BETA1-4 : bond 0.05409 ( 1) link_BETA1-4 : angle 2.27361 ( 3) hydrogen bonds : bond 0.16936 ( 105) hydrogen bonds : angle 8.24625 ( 276) link_BETA1-6 : bond 0.04677 ( 1) link_BETA1-6 : angle 1.86634 ( 3) SS BOND : bond 0.02145 ( 3) SS BOND : angle 2.19574 ( 6) covalent geometry : bond 0.01211 ( 2804) covalent geometry : angle 1.19329 ( 3810) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.305 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.7154 time to fit residues: 63.9661 Evaluate side-chains 61 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.0870 chunk 25 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.0570 overall best weight: 0.0834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN L 33 ASN A 99 ASN A 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136227 restraints weight = 3525.924| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.17 r_work: 0.3483 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2811 Z= 0.122 Angle : 0.611 9.146 3828 Z= 0.315 Chirality : 0.044 0.187 427 Planarity : 0.004 0.034 479 Dihedral : 6.147 57.028 459 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.81 % Allowed : 11.93 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.90 (0.40), residues: 152 loop : 0.06 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 116 HIS 0.002 0.001 HIS L 41 PHE 0.012 0.002 PHE H 29 TYR 0.016 0.002 TYR A 248 ARG 0.006 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 2) link_NAG-ASN : angle 1.71435 ( 6) link_BETA1-4 : bond 0.00892 ( 1) link_BETA1-4 : angle 1.97157 ( 3) hydrogen bonds : bond 0.04439 ( 105) hydrogen bonds : angle 6.54928 ( 276) link_BETA1-6 : bond 0.00755 ( 1) link_BETA1-6 : angle 1.25693 ( 3) SS BOND : bond 0.00283 ( 3) SS BOND : angle 1.26589 ( 6) covalent geometry : bond 0.00258 ( 2804) covalent geometry : angle 0.60295 ( 3810) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.351 Fit side-chains REVERT: H 19 ARG cc_start: 0.8044 (ttt90) cc_final: 0.7843 (ttm170) REVERT: L 84 ASP cc_start: 0.8102 (m-30) cc_final: 0.7874 (m-30) outliers start: 8 outliers final: 4 residues processed: 71 average time/residue: 0.7417 time to fit residues: 54.9062 Evaluate side-chains 66 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 0.0000 chunk 29 optimal weight: 0.1980 chunk 3 optimal weight: 0.1980 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN L 33 ASN ** A 239 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 = 0.3557 r_free = 0.3557 target = 0.136856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.129211 restraints weight = 3541.427| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.13 r_work: 0.3402 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 2811 Z= 0.204 Angle : 0.641 7.514 3828 Z= 0.325 Chirality : 0.045 0.195 427 Planarity : 0.005 0.041 479 Dihedral : 5.958 49.286 459 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.21 % Allowed : 11.93 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.70 (0.41), residues: 152 loop : -0.11 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.014 0.002 PHE H 29 TYR 0.018 0.002 TYR A 248 ARG 0.006 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 2) link_NAG-ASN : angle 2.37980 ( 6) link_BETA1-4 : bond 0.00688 ( 1) link_BETA1-4 : angle 1.81301 ( 3) hydrogen bonds : bond 0.03907 ( 105) hydrogen bonds : angle 6.22138 ( 276) link_BETA1-6 : bond 0.00169 ( 1) link_BETA1-6 : angle 1.80825 ( 3) SS BOND : bond 0.00749 ( 3) SS BOND : angle 1.00197 ( 6) covalent geometry : bond 0.00450 ( 2804) covalent geometry : angle 0.63071 ( 3810) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.312 Fit side-chains REVERT: L 84 ASP cc_start: 0.8190 (m-30) cc_final: 0.7989 (m-30) REVERT: A 122 ASN cc_start: 0.7693 (p0) cc_final: 0.7476 (p0) outliers start: 12 outliers final: 10 residues processed: 77 average time/residue: 0.6783 time to fit residues: 54.4910 Evaluate side-chains 72 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.0370 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN L 41 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128525 restraints weight = 3579.693| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.19 r_work: 0.3399 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 2811 Z= 0.187 Angle : 0.613 7.438 3828 Z= 0.313 Chirality : 0.045 0.216 427 Planarity : 0.005 0.047 479 Dihedral : 5.628 37.382 459 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.51 % Allowed : 14.04 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.49 (0.42), residues: 154 loop : -0.14 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 64 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.002 PHE H 29 TYR 0.021 0.002 TYR A 248 ARG 0.008 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00116 ( 2) link_NAG-ASN : angle 2.66195 ( 6) link_BETA1-4 : bond 0.00536 ( 1) link_BETA1-4 : angle 1.59993 ( 3) hydrogen bonds : bond 0.03565 ( 105) hydrogen bonds : angle 6.22767 ( 276) link_BETA1-6 : bond 0.00136 ( 1) link_BETA1-6 : angle 1.90453 ( 3) SS BOND : bond 0.00434 ( 3) SS BOND : angle 1.08016 ( 6) covalent geometry : bond 0.00420 ( 2804) covalent geometry : angle 0.59994 ( 3810) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.427 Fit side-chains REVERT: L 84 ASP cc_start: 0.8275 (m-30) cc_final: 0.8054 (m-30) REVERT: A 20 THR cc_start: 0.8613 (p) cc_final: 0.8382 (p) REVERT: A 153 MET cc_start: 0.8268 (mtt) cc_final: 0.8059 (mtt) outliers start: 10 outliers final: 6 residues processed: 71 average time/residue: 0.8028 time to fit residues: 59.4719 Evaluate side-chains 66 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 10 optimal weight: 0.0770 chunk 2 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 overall best weight: 0.1938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 84 ASN H 118 GLN A 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.136000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128627 restraints weight = 3626.771| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.11 r_work: 0.3412 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2811 Z= 0.141 Angle : 0.576 7.584 3828 Z= 0.296 Chirality : 0.043 0.225 427 Planarity : 0.004 0.043 479 Dihedral : 5.198 33.280 459 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.21 % Allowed : 15.79 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.11 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.45 (0.42), residues: 154 loop : -0.18 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 116 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE H 29 TYR 0.020 0.001 TYR A 248 ARG 0.008 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 2) link_NAG-ASN : angle 2.50058 ( 6) link_BETA1-4 : bond 0.00459 ( 1) link_BETA1-4 : angle 1.47790 ( 3) hydrogen bonds : bond 0.03166 ( 105) hydrogen bonds : angle 6.00614 ( 276) link_BETA1-6 : bond 0.00291 ( 1) link_BETA1-6 : angle 1.79186 ( 3) SS BOND : bond 0.00320 ( 3) SS BOND : angle 1.05599 ( 6) covalent geometry : bond 0.00315 ( 2804) covalent geometry : angle 0.56309 ( 3810) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.302 Fit side-chains REVERT: H 52 SER cc_start: 0.9002 (p) cc_final: 0.8634 (t) REVERT: A 20 THR cc_start: 0.8502 (p) cc_final: 0.8245 (p) outliers start: 12 outliers final: 8 residues processed: 68 average time/residue: 0.7887 time to fit residues: 55.6708 Evaluate side-chains 71 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.0970 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 27 optimal weight: 0.0770 chunk 2 optimal weight: 0.0980 chunk 3 optimal weight: 0.3980 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129054 restraints weight = 3645.286| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.12 r_work: 0.3416 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2811 Z= 0.148 Angle : 0.572 7.620 3828 Z= 0.295 Chirality : 0.043 0.239 427 Planarity : 0.004 0.048 479 Dihedral : 5.067 29.972 459 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.51 % Allowed : 16.84 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.34 (0.42), residues: 154 loop : -0.19 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 152 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.002 PHE H 29 TYR 0.017 0.001 TYR A 248 ARG 0.009 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 2) link_NAG-ASN : angle 2.62118 ( 6) link_BETA1-4 : bond 0.00552 ( 1) link_BETA1-4 : angle 1.29998 ( 3) hydrogen bonds : bond 0.03174 ( 105) hydrogen bonds : angle 5.98215 ( 276) link_BETA1-6 : bond 0.00114 ( 1) link_BETA1-6 : angle 1.77827 ( 3) SS BOND : bond 0.00357 ( 3) SS BOND : angle 0.93546 ( 6) covalent geometry : bond 0.00333 ( 2804) covalent geometry : angle 0.55965 ( 3810) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.302 Fit side-chains REVERT: H 52 SER cc_start: 0.9019 (p) cc_final: 0.8675 (t) REVERT: A 20 THR cc_start: 0.8516 (p) cc_final: 0.8240 (p) outliers start: 10 outliers final: 8 residues processed: 73 average time/residue: 0.7272 time to fit residues: 55.1570 Evaluate side-chains 72 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 overall best weight: 0.2378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.134510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126802 restraints weight = 3703.016| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.13 r_work: 0.3407 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2811 Z= 0.159 Angle : 0.585 7.679 3828 Z= 0.301 Chirality : 0.044 0.236 427 Planarity : 0.004 0.056 479 Dihedral : 5.043 28.456 459 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.91 % Allowed : 17.19 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.37 (0.42), residues: 154 loop : -0.18 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 152 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.002 PHE H 29 TYR 0.016 0.001 TYR A 248 ARG 0.009 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00123 ( 2) link_NAG-ASN : angle 2.61096 ( 6) link_BETA1-4 : bond 0.00541 ( 1) link_BETA1-4 : angle 1.26345 ( 3) hydrogen bonds : bond 0.03232 ( 105) hydrogen bonds : angle 6.04735 ( 276) link_BETA1-6 : bond 0.00231 ( 1) link_BETA1-6 : angle 1.83693 ( 3) SS BOND : bond 0.00422 ( 3) SS BOND : angle 1.06923 ( 6) covalent geometry : bond 0.00358 ( 2804) covalent geometry : angle 0.57249 ( 3810) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.307 Fit side-chains REVERT: H 52 SER cc_start: 0.9018 (p) cc_final: 0.8684 (t) REVERT: A 20 THR cc_start: 0.8494 (p) cc_final: 0.8261 (p) outliers start: 14 outliers final: 10 residues processed: 75 average time/residue: 0.7070 time to fit residues: 55.1799 Evaluate side-chains 73 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 1 optimal weight: 0.2980 chunk 20 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.0470 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 26 optimal weight: 0.2980 overall best weight: 0.2678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126533 restraints weight = 3622.036| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.12 r_work: 0.3411 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2811 Z= 0.173 Angle : 0.599 7.800 3828 Z= 0.309 Chirality : 0.045 0.247 427 Planarity : 0.004 0.025 479 Dihedral : 5.132 28.436 459 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.86 % Allowed : 18.60 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.34 (0.43), residues: 154 loop : -0.18 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 152 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.002 PHE H 29 TYR 0.015 0.002 TYR H 95 ARG 0.007 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 2) link_NAG-ASN : angle 2.63564 ( 6) link_BETA1-4 : bond 0.00514 ( 1) link_BETA1-4 : angle 1.19621 ( 3) hydrogen bonds : bond 0.03237 ( 105) hydrogen bonds : angle 6.11530 ( 276) link_BETA1-6 : bond 0.00199 ( 1) link_BETA1-6 : angle 1.91208 ( 3) SS BOND : bond 0.00361 ( 3) SS BOND : angle 1.20506 ( 6) covalent geometry : bond 0.00391 ( 2804) covalent geometry : angle 0.58599 ( 3810) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.310 Fit side-chains REVERT: H 52 SER cc_start: 0.9024 (p) cc_final: 0.8677 (t) REVERT: A 20 THR cc_start: 0.8527 (p) cc_final: 0.8274 (p) outliers start: 11 outliers final: 9 residues processed: 71 average time/residue: 0.7875 time to fit residues: 58.0144 Evaluate side-chains 71 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.134535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.126914 restraints weight = 3613.248| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.10 r_work: 0.3400 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 2811 Z= 0.197 Angle : 0.632 7.886 3828 Z= 0.325 Chirality : 0.046 0.261 427 Planarity : 0.004 0.027 479 Dihedral : 5.380 34.823 459 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.86 % Allowed : 19.30 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.27 (0.43), residues: 154 loop : -0.29 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 258 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.002 PHE H 29 TYR 0.016 0.002 TYR A 248 ARG 0.005 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 2) link_NAG-ASN : angle 2.74588 ( 6) link_BETA1-4 : bond 0.00542 ( 1) link_BETA1-4 : angle 1.12633 ( 3) hydrogen bonds : bond 0.03316 ( 105) hydrogen bonds : angle 6.27142 ( 276) link_BETA1-6 : bond 0.00156 ( 1) link_BETA1-6 : angle 1.98667 ( 3) SS BOND : bond 0.00378 ( 3) SS BOND : angle 1.18041 ( 6) covalent geometry : bond 0.00445 ( 2804) covalent geometry : angle 0.61939 ( 3810) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.279 Fit side-chains REVERT: L 84 ASP cc_start: 0.8157 (m-30) cc_final: 0.7910 (m-30) REVERT: A 20 THR cc_start: 0.8472 (p) cc_final: 0.8224 (p) outliers start: 11 outliers final: 10 residues processed: 70 average time/residue: 0.7992 time to fit residues: 57.9598 Evaluate side-chains 74 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 chunk 28 optimal weight: 0.0970 chunk 31 optimal weight: 0.0980 chunk 23 optimal weight: 0.0050 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 4 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 overall best weight: 0.0930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.138988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131163 restraints weight = 3571.547| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.16 r_work: 0.3440 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2811 Z= 0.110 Angle : 0.579 7.937 3828 Z= 0.299 Chirality : 0.043 0.214 427 Planarity : 0.004 0.029 479 Dihedral : 4.639 25.142 459 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.81 % Allowed : 21.40 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.42 (0.44), residues: 144 loop : -0.18 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 152 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE A 238 TYR 0.013 0.001 TYR A 248 ARG 0.006 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 2) link_NAG-ASN : angle 2.34118 ( 6) link_BETA1-4 : bond 0.00614 ( 1) link_BETA1-4 : angle 1.03144 ( 3) hydrogen bonds : bond 0.02812 ( 105) hydrogen bonds : angle 5.70295 ( 276) link_BETA1-6 : bond 0.00237 ( 1) link_BETA1-6 : angle 1.64000 ( 3) SS BOND : bond 0.00312 ( 3) SS BOND : angle 1.09490 ( 6) covalent geometry : bond 0.00250 ( 2804) covalent geometry : angle 0.56857 ( 3810) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.283 Fit side-chains REVERT: H 52 SER cc_start: 0.8994 (p) cc_final: 0.8692 (t) REVERT: A 20 THR cc_start: 0.8448 (p) cc_final: 0.8192 (p) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.7682 time to fit residues: 54.1638 Evaluate side-chains 69 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 chunk 29 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN A 137 ASN A 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.134022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.125546 restraints weight = 3507.452| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.25 r_work: 0.3362 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 2811 Z= 0.238 Angle : 0.673 8.993 3828 Z= 0.349 Chirality : 0.047 0.267 427 Planarity : 0.005 0.048 479 Dihedral : 5.468 36.347 459 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.16 % Allowed : 21.05 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.21 (0.44), residues: 154 loop : -0.42 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 258 HIS 0.005 0.001 HIS H 35 PHE 0.017 0.002 PHE H 29 TYR 0.017 0.002 TYR H 95 ARG 0.009 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 2) link_NAG-ASN : angle 2.78216 ( 6) link_BETA1-4 : bond 0.00586 ( 1) link_BETA1-4 : angle 1.03813 ( 3) hydrogen bonds : bond 0.03582 ( 105) hydrogen bonds : angle 6.40521 ( 276) link_BETA1-6 : bond 0.00211 ( 1) link_BETA1-6 : angle 2.02974 ( 3) SS BOND : bond 0.00409 ( 3) SS BOND : angle 1.16034 ( 6) covalent geometry : bond 0.00542 ( 2804) covalent geometry : angle 0.66125 ( 3810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2775.52 seconds wall clock time: 48 minutes 5.51 seconds (2885.51 seconds total)