Starting phenix.real_space_refine on Wed Jul 23 10:09:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ly0_23581/07_2025/7ly0_23581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ly0_23581/07_2025/7ly0_23581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ly0_23581/07_2025/7ly0_23581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ly0_23581/07_2025/7ly0_23581.map" model { file = "/net/cci-nas-00/data/ceres_data/7ly0_23581/07_2025/7ly0_23581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ly0_23581/07_2025/7ly0_23581.cif" } resolution = 2.6 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= 0.039 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 1796 2.51 5 N 463 2.21 5 O 536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 2805 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1033 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain breaks: 7 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 785 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'FUC': 1, 'MAN': 1, 'NAG': 2} 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: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.74, per 1000 atoms: 1.33 Number of scatterers: 2805 At special positions: 0 Unit cell: (73.5, 71.4, 74.55, 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 536 8.00 N 463 7.00 C 1796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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 ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 149 " " NAG B 1 " - " ASN A 17 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 336.9 milliseconds 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 650 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 7.6% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.185A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.544A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.445A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 95 Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.467A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.467A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.710A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.002A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) 103 hydrogen bonds defined for protein. 225 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: 0.75 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 520 1.32 - 1.45: 807 1.45 - 1.57: 1528 1.57 - 1.70: 4 1.70 - 1.82: 13 Bond restraints: 2872 Sorted by residual: bond pdb=" N TRP H 104 " pdb=" CA TRP H 104 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.16e-02 7.43e+03 8.17e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" CB ILE A 235 " pdb=" CG1 ILE A 235 " ideal model delta sigma weight residual 1.530 1.584 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" CG ASP A 138 " pdb=" OD1 ASP A 138 " ideal model delta sigma weight residual 1.249 1.198 0.051 1.90e-02 2.77e+03 7.23e+00 ... (remaining 2867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 3280 1.46 - 2.92: 518 2.92 - 4.38: 68 4.38 - 5.84: 25 5.84 - 7.30: 14 Bond angle restraints: 3905 Sorted by residual: angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 125.78 -6.12 7.30e-01 1.88e+00 7.02e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.32 -7.29 9.90e-01 1.02e+00 5.42e+01 angle pdb=" C ILE L 57 " pdb=" N PRO L 58 " pdb=" CA PRO L 58 " ideal model delta sigma weight residual 120.03 126.82 -6.79 9.90e-01 1.02e+00 4.71e+01 angle pdb=" C ARG L 53 " pdb=" N PRO L 54 " pdb=" CA PRO L 54 " ideal model delta sigma weight residual 119.92 127.22 -7.30 1.07e+00 8.73e-01 4.65e+01 angle pdb=" C PRO L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta sigma weight residual 119.19 126.17 -6.98 1.06e+00 8.90e-01 4.33e+01 ... (remaining 3900 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.83: 1668 17.83 - 35.65: 39 35.65 - 53.48: 14 53.48 - 71.30: 3 71.30 - 89.12: 1 Dihedral angle restraints: 1725 sinusoidal: 708 harmonic: 1017 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 51.87 41.13 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 87 " pdb=" CB CYS L 87 " ideal model delta sinusoidal sigma weight residual 93.00 55.35 37.65 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CA ARG L 53 " pdb=" C ARG L 53 " pdb=" N PRO L 54 " pdb=" CA PRO L 54 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 1722 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.062: 296 0.062 - 0.124: 104 0.124 - 0.186: 29 0.186 - 0.248: 16 0.248 - 0.309: 5 Chirality restraints: 450 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 -2.53 0.13 2.00e-02 2.50e+03 4.24e+01 chirality pdb=" C1 MAN B 3 " pdb=" O4 NAG B 2 " pdb=" C2 MAN B 3 " pdb=" O5 MAN B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.47 -0.07 2.00e-02 2.50e+03 1.19e+01 chirality pdb=" C1 FUC B 4 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 4 " pdb=" O5 FUC B 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.82e+00 ... (remaining 447 not shown) Planarity restraints: 484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 33 " 0.035 2.00e-02 2.50e+03 1.89e-02 7.18e+00 pdb=" CG TYR L 33 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR L 33 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR L 33 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR L 33 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR L 33 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR L 33 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 33 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 122 " 0.024 2.00e-02 2.50e+03 2.31e-02 6.67e+00 pdb=" CG ASN A 122 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 122 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 122 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 103 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C GLU H 103 " 0.032 2.00e-02 2.50e+03 pdb=" O GLU H 103 " -0.012 2.00e-02 2.50e+03 pdb=" N TRP H 104 " -0.011 2.00e-02 2.50e+03 ... (remaining 481 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1504 2.99 - 3.47: 2388 3.47 - 3.95: 4816 3.95 - 4.42: 5482 4.42 - 4.90: 8858 Nonbonded interactions: 23048 Sorted by model distance: nonbonded pdb=" NZ LYS A 77 " pdb=" O THR A 250 " model vdw 2.515 3.120 nonbonded pdb=" NZ LYS A 147 " pdb=" O LEU L 27 " model vdw 2.575 3.120 nonbonded pdb=" OD1 ASP L 91 " pdb=" N GLY L 94 " model vdw 2.576 3.120 nonbonded pdb=" OD1 ASP H 107 " pdb=" N TYR H 108 " model vdw 2.577 3.120 nonbonded pdb=" OG SER A 155 " pdb=" N GLU A 156 " model vdw 2.591 3.120 ... (remaining 23043 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: 5.400 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.590 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:14.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 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 0.067 2881 Z= 0.646 Angle : 1.198 7.298 3929 Z= 0.800 Chirality : 0.080 0.309 450 Planarity : 0.005 0.019 481 Dihedral : 9.438 89.124 1066 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.36 % Allowed : 0.36 % Favored : 99.29 % 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: 1.70 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 1.04 (0.39), residues: 154 loop : 1.42 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP L 34 HIS 0.002 0.001 HIS A 146 PHE 0.014 0.003 PHE A 175 TYR 0.035 0.004 TYR L 33 ARG 0.004 0.001 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.05587 ( 3) link_NAG-ASN : angle 2.16031 ( 9) link_ALPHA1-4 : bond 0.06677 ( 1) link_ALPHA1-4 : angle 3.07699 ( 3) link_BETA1-4 : bond 0.06179 ( 1) link_BETA1-4 : angle 3.03880 ( 3) hydrogen bonds : bond 0.12230 ( 94) hydrogen bonds : angle 8.05201 ( 225) link_BETA1-6 : bond 0.04555 ( 1) link_BETA1-6 : angle 1.44181 ( 3) SS BOND : bond 0.00404 ( 3) SS BOND : angle 2.38100 ( 6) covalent geometry : bond 0.01191 ( 2872) covalent geometry : angle 1.18702 ( 3905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.314 Fit side-chains REVERT: A 19 THR cc_start: 0.7681 (m) cc_final: 0.7459 (m) REVERT: A 86 PHE cc_start: 0.8153 (t80) cc_final: 0.7943 (t80) REVERT: L 20 ILE cc_start: 0.7448 (mt) cc_final: 0.7151 (mp) REVERT: L 31 TYR cc_start: 0.8175 (m-80) cc_final: 0.7627 (m-80) REVERT: L 53 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7921 (mtm110) REVERT: L 86 TYR cc_start: 0.8811 (m-80) cc_final: 0.8570 (m-80) REVERT: L 98 VAL cc_start: 0.8630 (p) cc_final: 0.8395 (t) REVERT: H 18 LEU cc_start: 0.7209 (tt) cc_final: 0.7004 (tp) REVERT: H 27 PHE cc_start: 0.7322 (p90) cc_final: 0.6992 (p90) REVERT: H 45 LEU cc_start: 0.8886 (mt) cc_final: 0.8563 (mt) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.6892 time to fit residues: 69.5160 Evaluate side-chains 77 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 0.2980 chunk 25 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 17 optimal weight: 0.4980 chunk 13 optimal weight: 0.0770 chunk 26 optimal weight: 0.0980 chunk 10 optimal weight: 0.0670 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 overall best weight: 0.1076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.191386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.186143 restraints weight = 2818.716| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 0.67 r_work: 0.3949 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.3885 rms_B_bonded: 1.71 restraints_weight: 0.2500 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2881 Z= 0.124 Angle : 0.558 6.142 3929 Z= 0.284 Chirality : 0.044 0.161 450 Planarity : 0.004 0.034 481 Dihedral : 4.513 21.153 504 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.86 % Allowed : 11.43 % Favored : 85.71 % 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: 1.79 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 1.18 (0.41), residues: 146 loop : 1.40 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 34 HIS 0.004 0.001 HIS A 245 PHE 0.008 0.001 PHE A 157 TYR 0.009 0.001 TYR H 95 ARG 0.003 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 3) link_NAG-ASN : angle 1.60870 ( 9) link_ALPHA1-4 : bond 0.01904 ( 1) link_ALPHA1-4 : angle 2.80030 ( 3) link_BETA1-4 : bond 0.00698 ( 1) link_BETA1-4 : angle 2.00381 ( 3) hydrogen bonds : bond 0.03350 ( 94) hydrogen bonds : angle 6.36275 ( 225) link_BETA1-6 : bond 0.00365 ( 1) link_BETA1-6 : angle 1.38002 ( 3) SS BOND : bond 0.00119 ( 3) SS BOND : angle 0.32570 ( 6) covalent geometry : bond 0.00283 ( 2872) covalent geometry : angle 0.54485 ( 3905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.270 Fit side-chains REVERT: A 19 THR cc_start: 0.8040 (m) cc_final: 0.7733 (m) REVERT: A 86 PHE cc_start: 0.8355 (t80) cc_final: 0.8090 (t80) REVERT: A 190 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6789 (mtt-85) REVERT: L 31 TYR cc_start: 0.8266 (m-80) cc_final: 0.7927 (m-80) outliers start: 8 outliers final: 4 residues processed: 89 average time/residue: 0.6832 time to fit residues: 63.3399 Evaluate side-chains 78 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain H residue 106 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 0.0050 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.0670 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.181396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.176037 restraints weight = 2768.203| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 0.66 r_work: 0.3831 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 2881 Z= 0.254 Angle : 0.685 6.943 3929 Z= 0.349 Chirality : 0.047 0.183 450 Planarity : 0.005 0.045 481 Dihedral : 5.013 21.220 504 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.64 % Allowed : 13.93 % Favored : 81.43 % 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: 1.01 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.61 (0.42), residues: 147 loop : 0.91 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS A 245 PHE 0.016 0.002 PHE A 133 TYR 0.014 0.002 TYR L 31 ARG 0.006 0.001 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 3) link_NAG-ASN : angle 2.36711 ( 9) link_ALPHA1-4 : bond 0.01779 ( 1) link_ALPHA1-4 : angle 2.56908 ( 3) link_BETA1-4 : bond 0.00546 ( 1) link_BETA1-4 : angle 1.64790 ( 3) hydrogen bonds : bond 0.04032 ( 94) hydrogen bonds : angle 6.39689 ( 225) link_BETA1-6 : bond 0.00164 ( 1) link_BETA1-6 : angle 1.23268 ( 3) SS BOND : bond 0.00754 ( 3) SS BOND : angle 1.79953 ( 6) covalent geometry : bond 0.00579 ( 2872) covalent geometry : angle 0.66735 ( 3905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.311 Fit side-chains REVERT: A 86 PHE cc_start: 0.8286 (t80) cc_final: 0.8083 (t80) REVERT: A 190 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6907 (mtt-85) REVERT: A 248 TYR cc_start: 0.8355 (t80) cc_final: 0.8152 (t80) REVERT: L 9 SER cc_start: 0.5599 (p) cc_final: 0.4990 (t) REVERT: L 31 TYR cc_start: 0.8603 (m-80) cc_final: 0.7909 (m-80) REVERT: H 27 PHE cc_start: 0.7543 (p90) cc_final: 0.7305 (p90) outliers start: 13 outliers final: 7 residues processed: 94 average time/residue: 0.6529 time to fit residues: 64.0067 Evaluate side-chains 84 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 10 optimal weight: 0.4980 chunk 13 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 25 optimal weight: 0.2980 chunk 8 optimal weight: 0.4980 chunk 23 optimal weight: 0.4980 chunk 33 optimal weight: 0.0870 chunk 14 optimal weight: 0.0370 chunk 29 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 overall best weight: 0.1836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.182681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.177233 restraints weight = 2848.605| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 0.68 r_work: 0.3835 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2881 Z= 0.140 Angle : 0.567 5.619 3929 Z= 0.289 Chirality : 0.044 0.160 450 Planarity : 0.004 0.039 481 Dihedral : 4.557 19.079 504 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 5.00 % Allowed : 15.71 % Favored : 79.29 % 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: 0.92 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.63 (0.41), residues: 152 loop : 0.77 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 34 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE A 133 TYR 0.011 0.001 TYR L 31 ARG 0.003 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 3) link_NAG-ASN : angle 1.83971 ( 9) link_ALPHA1-4 : bond 0.01701 ( 1) link_ALPHA1-4 : angle 2.56894 ( 3) link_BETA1-4 : bond 0.00461 ( 1) link_BETA1-4 : angle 1.63820 ( 3) hydrogen bonds : bond 0.03236 ( 94) hydrogen bonds : angle 6.06153 ( 225) link_BETA1-6 : bond 0.00293 ( 1) link_BETA1-6 : angle 1.17397 ( 3) SS BOND : bond 0.00074 ( 3) SS BOND : angle 2.30258 ( 6) covalent geometry : bond 0.00320 ( 2872) covalent geometry : angle 0.54680 ( 3905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.306 Fit side-chains REVERT: A 86 PHE cc_start: 0.8230 (t80) cc_final: 0.8022 (t80) REVERT: A 190 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6894 (mtt-85) REVERT: L 31 TYR cc_start: 0.8422 (m-80) cc_final: 0.8005 (m-80) REVERT: H 27 PHE cc_start: 0.7478 (p90) cc_final: 0.7249 (p90) outliers start: 14 outliers final: 11 residues processed: 77 average time/residue: 0.8229 time to fit residues: 65.6718 Evaluate side-chains 80 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 0.0670 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 30 optimal weight: 0.4980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.179558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.174104 restraints weight = 2798.805| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 0.66 r_work: 0.3811 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 2881 Z= 0.208 Angle : 0.621 6.144 3929 Z= 0.313 Chirality : 0.045 0.157 450 Planarity : 0.005 0.044 481 Dihedral : 4.910 19.938 504 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 6.07 % Allowed : 15.00 % Favored : 78.93 % 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: 0.26 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.15 (0.41), residues: 146 loop : 0.35 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE A 133 TYR 0.029 0.002 TYR A 248 ARG 0.003 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 3) link_NAG-ASN : angle 2.09658 ( 9) link_ALPHA1-4 : bond 0.01815 ( 1) link_ALPHA1-4 : angle 2.43519 ( 3) link_BETA1-4 : bond 0.00485 ( 1) link_BETA1-4 : angle 1.68675 ( 3) hydrogen bonds : bond 0.03515 ( 94) hydrogen bonds : angle 6.16449 ( 225) link_BETA1-6 : bond 0.00140 ( 1) link_BETA1-6 : angle 1.10993 ( 3) SS BOND : bond 0.00147 ( 3) SS BOND : angle 2.75564 ( 6) covalent geometry : bond 0.00472 ( 2872) covalent geometry : angle 0.59899 ( 3905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.287 Fit side-chains REVERT: A 190 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6979 (mtt-85) REVERT: L 31 TYR cc_start: 0.8458 (m-80) cc_final: 0.8104 (m-80) REVERT: H 27 PHE cc_start: 0.7549 (p90) cc_final: 0.7323 (p90) REVERT: H 80 TYR cc_start: 0.7231 (m-80) cc_final: 0.6825 (m-80) outliers start: 17 outliers final: 10 residues processed: 82 average time/residue: 0.7824 time to fit residues: 66.5129 Evaluate side-chains 84 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.180028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.174470 restraints weight = 2810.707| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 0.69 r_work: 0.3829 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 1.71 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 2881 Z= 0.244 Angle : 0.674 6.918 3929 Z= 0.335 Chirality : 0.048 0.184 450 Planarity : 0.005 0.045 481 Dihedral : 5.133 18.399 504 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 5.36 % Allowed : 18.21 % Favored : 76.43 % 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: 0.21 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.22 (0.41), residues: 144 loop : 0.21 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 47 HIS 0.004 0.001 HIS A 245 PHE 0.014 0.002 PHE A 133 TYR 0.027 0.002 TYR A 248 ARG 0.003 0.001 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 3) link_NAG-ASN : angle 2.28310 ( 9) link_ALPHA1-4 : bond 0.01696 ( 1) link_ALPHA1-4 : angle 2.38397 ( 3) link_BETA1-4 : bond 0.00462 ( 1) link_BETA1-4 : angle 1.81432 ( 3) hydrogen bonds : bond 0.03665 ( 94) hydrogen bonds : angle 6.35070 ( 225) link_BETA1-6 : bond 0.00270 ( 1) link_BETA1-6 : angle 1.08393 ( 3) SS BOND : bond 0.00263 ( 3) SS BOND : angle 3.52687 ( 6) covalent geometry : bond 0.00558 ( 2872) covalent geometry : angle 0.64620 ( 3905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.314 Fit side-chains REVERT: A 190 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6934 (mtt-85) REVERT: L 31 TYR cc_start: 0.8551 (m-80) cc_final: 0.7979 (m-80) REVERT: H 80 TYR cc_start: 0.7275 (m-80) cc_final: 0.6854 (m-80) outliers start: 15 outliers final: 10 residues processed: 82 average time/residue: 0.7804 time to fit residues: 66.3188 Evaluate side-chains 84 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 17 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.179398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.173850 restraints weight = 2833.212| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 0.68 r_work: 0.3825 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 1.66 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 2881 Z= 0.266 Angle : 0.697 7.110 3929 Z= 0.351 Chirality : 0.049 0.191 450 Planarity : 0.005 0.045 481 Dihedral : 5.305 18.658 504 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 6.07 % Allowed : 17.86 % Favored : 76.07 % 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 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.02 (0.41), residues: 145 loop : 0.16 (0.49), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 52 HIS 0.004 0.002 HIS A 245 PHE 0.015 0.002 PHE A 133 TYR 0.025 0.002 TYR A 248 ARG 0.003 0.001 ARG L 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 3) link_NAG-ASN : angle 2.44579 ( 9) link_ALPHA1-4 : bond 0.01710 ( 1) link_ALPHA1-4 : angle 2.32173 ( 3) link_BETA1-4 : bond 0.00553 ( 1) link_BETA1-4 : angle 1.86813 ( 3) hydrogen bonds : bond 0.03741 ( 94) hydrogen bonds : angle 6.47147 ( 225) link_BETA1-6 : bond 0.00208 ( 1) link_BETA1-6 : angle 1.03826 ( 3) SS BOND : bond 0.00253 ( 3) SS BOND : angle 3.29118 ( 6) covalent geometry : bond 0.00613 ( 2872) covalent geometry : angle 0.67163 ( 3905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.286 Fit side-chains REVERT: H 43 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7849 (mmtm) REVERT: H 80 TYR cc_start: 0.7337 (m-80) cc_final: 0.6909 (m-80) outliers start: 17 outliers final: 13 residues processed: 82 average time/residue: 0.9677 time to fit residues: 82.1288 Evaluate side-chains 86 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 13 optimal weight: 0.0670 chunk 17 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.0050 chunk 14 optimal weight: 0.0040 chunk 25 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 0.0020 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 overall best weight: 0.0752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.183152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.177647 restraints weight = 2812.644| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 0.67 r_work: 0.3851 rms_B_bonded: 0.98 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2881 Z= 0.107 Angle : 0.558 5.313 3929 Z= 0.288 Chirality : 0.045 0.194 450 Planarity : 0.004 0.039 481 Dihedral : 4.549 18.204 504 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.57 % Allowed : 20.00 % Favored : 76.43 % 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: 0.46 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.37 (0.40), residues: 143 loop : 0.39 (0.49), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 152 HIS 0.003 0.001 HIS A 146 PHE 0.006 0.001 PHE A 157 TYR 0.025 0.001 TYR A 248 ARG 0.002 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 3) link_NAG-ASN : angle 1.51278 ( 9) link_ALPHA1-4 : bond 0.01628 ( 1) link_ALPHA1-4 : angle 2.33232 ( 3) link_BETA1-4 : bond 0.00295 ( 1) link_BETA1-4 : angle 1.68418 ( 3) hydrogen bonds : bond 0.02929 ( 94) hydrogen bonds : angle 6.03213 ( 225) link_BETA1-6 : bond 0.00410 ( 1) link_BETA1-6 : angle 1.18444 ( 3) SS BOND : bond 0.00188 ( 3) SS BOND : angle 2.28175 ( 6) covalent geometry : bond 0.00235 ( 2872) covalent geometry : angle 0.54114 ( 3905) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.302 Fit side-chains REVERT: L 31 TYR cc_start: 0.8462 (m-80) cc_final: 0.8066 (m-10) REVERT: H 80 TYR cc_start: 0.7166 (m-80) cc_final: 0.6804 (m-80) outliers start: 10 outliers final: 5 residues processed: 79 average time/residue: 0.7220 time to fit residues: 59.2981 Evaluate side-chains 74 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.0010 chunk 15 optimal weight: 0.1980 chunk 24 optimal weight: 0.0050 overall best weight: 0.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.188413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.182672 restraints weight = 2934.098| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 0.73 r_work: 0.3922 rms_B_bonded: 1.03 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2881 Z= 0.127 Angle : 0.585 5.476 3929 Z= 0.297 Chirality : 0.045 0.171 450 Planarity : 0.004 0.041 481 Dihedral : 4.543 19.468 504 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.14 % Allowed : 23.21 % Favored : 74.64 % 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: 0.55 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.44 (0.40), residues: 143 loop : 0.44 (0.49), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.003 0.001 HIS A 146 PHE 0.017 0.001 PHE H 27 TYR 0.026 0.002 TYR A 248 ARG 0.002 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 3) link_NAG-ASN : angle 1.57317 ( 9) link_ALPHA1-4 : bond 0.01542 ( 1) link_ALPHA1-4 : angle 2.19868 ( 3) link_BETA1-4 : bond 0.00478 ( 1) link_BETA1-4 : angle 1.63779 ( 3) hydrogen bonds : bond 0.02932 ( 94) hydrogen bonds : angle 5.95687 ( 225) link_BETA1-6 : bond 0.00345 ( 1) link_BETA1-6 : angle 1.14101 ( 3) SS BOND : bond 0.00288 ( 3) SS BOND : angle 2.94581 ( 6) covalent geometry : bond 0.00291 ( 2872) covalent geometry : angle 0.56445 ( 3905) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.275 Fit side-chains REVERT: L 31 TYR cc_start: 0.8500 (m-80) cc_final: 0.8134 (m-80) REVERT: H 80 TYR cc_start: 0.7207 (m-80) cc_final: 0.6864 (m-80) outliers start: 6 outliers final: 6 residues processed: 72 average time/residue: 0.7283 time to fit residues: 54.5929 Evaluate side-chains 71 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 0.0570 chunk 19 optimal weight: 0.0370 chunk 25 optimal weight: 0.3980 chunk 31 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.0970 chunk 5 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.1352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.184444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.179044 restraints weight = 2847.819| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 0.67 r_work: 0.3859 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2881 Z= 0.119 Angle : 0.572 5.586 3929 Z= 0.292 Chirality : 0.044 0.165 450 Planarity : 0.004 0.039 481 Dihedral : 4.407 18.660 504 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.79 % Allowed : 24.29 % Favored : 73.93 % 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: 0.58 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.49 (0.40), residues: 145 loop : 0.45 (0.50), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 109 HIS 0.002 0.001 HIS H 35 PHE 0.014 0.001 PHE H 27 TYR 0.025 0.001 TYR A 248 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 3) link_NAG-ASN : angle 1.42407 ( 9) link_ALPHA1-4 : bond 0.01483 ( 1) link_ALPHA1-4 : angle 2.14834 ( 3) link_BETA1-4 : bond 0.00493 ( 1) link_BETA1-4 : angle 1.62096 ( 3) hydrogen bonds : bond 0.02885 ( 94) hydrogen bonds : angle 5.81327 ( 225) link_BETA1-6 : bond 0.00348 ( 1) link_BETA1-6 : angle 1.12901 ( 3) SS BOND : bond 0.00235 ( 3) SS BOND : angle 2.95436 ( 6) covalent geometry : bond 0.00272 ( 2872) covalent geometry : angle 0.55226 ( 3905) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.301 Fit side-chains REVERT: L 31 TYR cc_start: 0.8453 (m-80) cc_final: 0.8099 (m-80) REVERT: L 84 ASP cc_start: 0.7803 (m-30) cc_final: 0.7552 (m-30) outliers start: 5 outliers final: 5 residues processed: 71 average time/residue: 0.7006 time to fit residues: 51.8591 Evaluate side-chains 70 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.0970 chunk 7 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.185799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.179704 restraints weight = 2887.890| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 0.75 r_work: 0.3886 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 2881 Z= 0.223 Angle : 0.661 7.314 3929 Z= 0.332 Chirality : 0.048 0.179 450 Planarity : 0.005 0.044 481 Dihedral : 4.893 18.691 504 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.50 % Allowed : 22.86 % Favored : 74.64 % 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 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.22 (0.41), residues: 145 loop : 0.24 (0.49), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 52 HIS 0.003 0.002 HIS A 146 PHE 0.012 0.002 PHE H 27 TYR 0.027 0.002 TYR A 248 ARG 0.005 0.001 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00114 ( 3) link_NAG-ASN : angle 1.92804 ( 9) link_ALPHA1-4 : bond 0.01525 ( 1) link_ALPHA1-4 : angle 2.02531 ( 3) link_BETA1-4 : bond 0.00523 ( 1) link_BETA1-4 : angle 1.73649 ( 3) hydrogen bonds : bond 0.03381 ( 94) hydrogen bonds : angle 6.22023 ( 225) link_BETA1-6 : bond 0.00314 ( 1) link_BETA1-6 : angle 1.04993 ( 3) SS BOND : bond 0.00300 ( 3) SS BOND : angle 3.19153 ( 6) covalent geometry : bond 0.00514 ( 2872) covalent geometry : angle 0.63992 ( 3905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2989.40 seconds wall clock time: 51 minutes 39.51 seconds (3099.51 seconds total)