Starting phenix.real_space_refine on Wed Jul 23 21:34:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sj0_25149/07_2025/7sj0_25149.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sj0_25149/07_2025/7sj0_25149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sj0_25149/07_2025/7sj0_25149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sj0_25149/07_2025/7sj0_25149.map" model { file = "/net/cci-nas-00/data/ceres_data/7sj0_25149/07_2025/7sj0_25149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sj0_25149/07_2025/7sj0_25149.cif" } resolution = 3.36 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 812 atoms to isotropic. 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 14 5.16 5 C 2279 2.51 5 N 593 2.21 5 O 704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3590 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1806 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 10, 'TRANS': 213} Chain breaks: 4 Chain: "B" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 784 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.85, per 1000 atoms: 1.07 Number of scatterers: 3590 At special positions: 0 Unit cell: (99, 78.1, 94.6, 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 14 16.00 O 704 8.00 N 593 7.00 C 2279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.04 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 NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 17 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 149 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 395.6 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 9 sheets defined 2.0% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'B' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 4.312A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 4.045A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS A 69 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.702A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 155 removed outlier: 4.000A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.735A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.846A pdb=" N THR B 119 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 118 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 92 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 99 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 33 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 40 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.525A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE L 76 " --> pdb=" O VAL L 18 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 46 through 50 removed outlier: 3.640A pdb=" N GLN L 38 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER L 35 " --> pdb=" O GLY L 90 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY L 90 " --> pdb=" O SER L 35 " (cutoff:3.500A) 93 hydrogen bonds defined for protein. 228 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: 0.87 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1130 1.34 - 1.46: 942 1.46 - 1.58: 1584 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3676 Sorted by residual: bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.94e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.56e+00 ... (remaining 3671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 4795 1.51 - 3.02: 173 3.02 - 4.53: 22 4.53 - 6.04: 4 6.04 - 7.54: 2 Bond angle restraints: 4996 Sorted by residual: angle pdb=" CA THR A 33 " pdb=" CB THR A 33 " pdb=" CG2 THR A 33 " ideal model delta sigma weight residual 110.50 114.45 -3.95 1.70e+00 3.46e-01 5.39e+00 angle pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 114.40 119.53 -5.13 2.30e+00 1.89e-01 4.98e+00 angle pdb=" CA LEU L 96 " pdb=" CB LEU L 96 " pdb=" CG LEU L 96 " ideal model delta sigma weight residual 116.30 123.84 -7.54 3.50e+00 8.16e-02 4.65e+00 angle pdb=" CB MET B 34 " pdb=" CG MET B 34 " pdb=" SD MET B 34 " ideal model delta sigma weight residual 112.70 118.84 -6.14 3.00e+00 1.11e-01 4.20e+00 angle pdb=" C PHE A 32 " pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta sigma weight residual 122.68 125.62 -2.94 1.47e+00 4.63e-01 4.01e+00 ... (remaining 4991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 2034 17.30 - 34.60: 135 34.60 - 51.90: 33 51.90 - 69.20: 8 69.20 - 86.49: 3 Dihedral angle restraints: 2213 sinusoidal: 922 harmonic: 1291 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -135.37 49.37 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CA ASN A 99 " pdb=" C ASN A 99 " pdb=" N ILE A 100 " pdb=" CA ILE A 100 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA THR A 167 " pdb=" C THR A 167 " pdb=" N PHE A 168 " pdb=" CA PHE A 168 " ideal model delta harmonic sigma weight residual -180.00 -157.25 -22.75 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 2210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 503 0.082 - 0.164: 60 0.164 - 0.246: 0 0.246 - 0.328: 1 0.328 - 0.410: 1 Chirality restraints: 565 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 562 not shown) Planarity restraints: 637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 55 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO L 56 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO L 56 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO L 56 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 99 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" C ASN A 99 " 0.021 2.00e-02 2.50e+03 pdb=" O ASN A 99 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE A 100 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " -0.010 2.00e-02 2.50e+03 9.87e-03 1.22e+00 pdb=" CG ASN A 61 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " 0.013 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.011 2.00e-02 2.50e+03 ... (remaining 634 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 512 2.76 - 3.30: 3344 3.30 - 3.83: 4986 3.83 - 4.37: 5454 4.37 - 4.90: 10160 Nonbonded interactions: 24456 Sorted by model distance: nonbonded pdb=" OG SER L 68 " pdb=" OG SER L 71 " model vdw 2.225 3.040 nonbonded pdb=" O GLY L 30 " pdb=" NZ LYS L 67 " model vdw 2.273 3.120 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.300 3.040 nonbonded pdb=" NZ LYS A 129 " pdb=" O PHE A 168 " model vdw 2.337 3.120 nonbonded pdb=" OG1 THR A 124 " pdb=" O7 NAG A1301 " model vdw 2.337 3.040 ... (remaining 24451 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: 5.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.030 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3685 Z= 0.150 Angle : 0.695 11.271 5019 Z= 0.340 Chirality : 0.052 0.410 565 Planarity : 0.004 0.030 632 Dihedral : 12.810 86.494 1377 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.98 (0.38), residues: 438 helix: None (None), residues: 0 sheet: -0.01 (0.42), residues: 141 loop : -2.13 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 108 HIS 0.001 0.000 HIS A 69 PHE 0.012 0.001 PHE A 238 TYR 0.010 0.001 TYR B 27 ARG 0.007 0.001 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.01028 ( 5) link_NAG-ASN : angle 4.20517 ( 15) hydrogen bonds : bond 0.31461 ( 83) hydrogen bonds : angle 10.57815 ( 228) SS BOND : bond 0.00359 ( 4) SS BOND : angle 1.09922 ( 8) covalent geometry : bond 0.00317 ( 3676) covalent geometry : angle 0.65582 ( 4996) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.385 Fit side-chains REVERT: A 69 HIS cc_start: 0.7608 (t-90) cc_final: 0.7232 (t-90) REVERT: A 128 ILE cc_start: 0.8539 (mp) cc_final: 0.8327 (mp) REVERT: A 144 TYR cc_start: 0.8296 (p90) cc_final: 0.8091 (p90) REVERT: A 202 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8367 (mtpt) REVERT: B 64 PHE cc_start: 0.8333 (m-10) cc_final: 0.8057 (m-10) REVERT: B 107 ASN cc_start: 0.7869 (p0) cc_final: 0.7609 (p0) REVERT: L 76 ILE cc_start: 0.8006 (tp) cc_final: 0.7749 (tt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1697 time to fit residues: 21.5887 Evaluate side-chains 94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.0040 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 99 ASN A 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.102833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.085796 restraints weight = 8831.656| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 4.20 r_work: 0.3198 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3685 Z= 0.198 Angle : 0.758 13.876 5019 Z= 0.380 Chirality : 0.055 0.543 565 Planarity : 0.005 0.033 632 Dihedral : 7.729 58.371 587 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.31 % Allowed : 11.83 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.74 (0.38), residues: 438 helix: None (None), residues: 0 sheet: 0.45 (0.42), residues: 144 loop : -2.17 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 108 HIS 0.003 0.001 HIS B 35 PHE 0.018 0.002 PHE A 86 TYR 0.015 0.002 TYR B 27 ARG 0.008 0.001 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.01234 ( 5) link_NAG-ASN : angle 4.92748 ( 15) hydrogen bonds : bond 0.05399 ( 83) hydrogen bonds : angle 7.10087 ( 228) SS BOND : bond 0.00789 ( 4) SS BOND : angle 1.61169 ( 8) covalent geometry : bond 0.00455 ( 3676) covalent geometry : angle 0.70743 ( 4996) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.396 Fit side-chains REVERT: A 128 ILE cc_start: 0.8686 (mp) cc_final: 0.8404 (mp) REVERT: A 172 SER cc_start: 0.7886 (t) cc_final: 0.7141 (m) REVERT: A 202 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8580 (mtpt) REVERT: B 62 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8307 (tm-30) REVERT: B 107 ASN cc_start: 0.8380 (p0) cc_final: 0.8119 (p0) REVERT: L 55 ARG cc_start: 0.7863 (ptm160) cc_final: 0.7562 (ptm160) outliers start: 9 outliers final: 4 residues processed: 101 average time/residue: 0.1788 time to fit residues: 21.5408 Evaluate side-chains 96 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 250 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 17 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 0.0030 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN L 28 ASN L 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.102982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085953 restraints weight = 8861.842| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 4.23 r_work: 0.3187 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3685 Z= 0.173 Angle : 0.715 13.019 5019 Z= 0.360 Chirality : 0.053 0.503 565 Planarity : 0.005 0.037 632 Dihedral : 7.760 58.815 587 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.57 % Allowed : 13.62 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.59 (0.38), residues: 438 helix: None (None), residues: 0 sheet: 0.53 (0.41), residues: 152 loop : -2.11 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 104 HIS 0.002 0.000 HIS B 35 PHE 0.014 0.002 PHE A 86 TYR 0.012 0.002 TYR B 27 ARG 0.008 0.001 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.01127 ( 5) link_NAG-ASN : angle 4.62526 ( 15) hydrogen bonds : bond 0.04679 ( 83) hydrogen bonds : angle 6.42695 ( 228) SS BOND : bond 0.00661 ( 4) SS BOND : angle 1.66027 ( 8) covalent geometry : bond 0.00396 ( 3676) covalent geometry : angle 0.66724 ( 4996) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.398 Fit side-chains REVERT: A 128 ILE cc_start: 0.8682 (mp) cc_final: 0.8443 (mp) REVERT: A 202 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8544 (mtpt) REVERT: B 6 GLN cc_start: 0.7796 (pm20) cc_final: 0.7578 (pm20) REVERT: B 107 ASN cc_start: 0.8501 (p0) cc_final: 0.8211 (p0) outliers start: 10 outliers final: 6 residues processed: 105 average time/residue: 0.1731 time to fit residues: 21.7494 Evaluate side-chains 99 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain L residue 23 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 33 optimal weight: 0.0870 chunk 39 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.103295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.086284 restraints weight = 8721.562| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 4.17 r_work: 0.3206 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3685 Z= 0.151 Angle : 0.695 12.166 5019 Z= 0.347 Chirality : 0.052 0.487 565 Planarity : 0.005 0.042 632 Dihedral : 7.452 59.749 587 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.60 % Allowed : 13.88 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.34 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.62 (0.40), residues: 167 loop : -2.03 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.002 0.001 HIS B 35 PHE 0.010 0.002 PHE L 101 TYR 0.010 0.001 TYR B 95 ARG 0.009 0.001 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.01069 ( 5) link_NAG-ASN : angle 4.37586 ( 15) hydrogen bonds : bond 0.04110 ( 83) hydrogen bonds : angle 6.03150 ( 228) SS BOND : bond 0.00651 ( 4) SS BOND : angle 1.45121 ( 8) covalent geometry : bond 0.00343 ( 3676) covalent geometry : angle 0.65163 ( 4996) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8697 (mp) cc_final: 0.8438 (mp) REVERT: A 195 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8806 (ttpp) REVERT: A 202 LYS cc_start: 0.8892 (mtpt) cc_final: 0.8530 (mtpt) REVERT: B 81 MET cc_start: 0.8890 (tmm) cc_final: 0.8653 (ttm) REVERT: B 107 ASN cc_start: 0.8500 (p0) cc_final: 0.8198 (p0) REVERT: L 54 LYS cc_start: 0.8476 (ttmm) cc_final: 0.8099 (tppt) REVERT: L 93 ASP cc_start: 0.9345 (t0) cc_final: 0.9120 (t0) outliers start: 14 outliers final: 8 residues processed: 102 average time/residue: 0.1849 time to fit residues: 22.4208 Evaluate side-chains 103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain L residue 23 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 35 optimal weight: 0.0060 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.102895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.085642 restraints weight = 8981.439| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 4.27 r_work: 0.3186 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3685 Z= 0.162 Angle : 0.705 11.909 5019 Z= 0.354 Chirality : 0.052 0.500 565 Planarity : 0.005 0.044 632 Dihedral : 7.226 59.846 587 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.11 % Allowed : 15.17 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.37 (0.39), residues: 438 helix: None (None), residues: 0 sheet: 0.79 (0.41), residues: 155 loop : -2.07 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.003 0.001 HIS B 35 PHE 0.013 0.002 PHE A 86 TYR 0.010 0.001 TYR B 95 ARG 0.010 0.001 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.01060 ( 5) link_NAG-ASN : angle 4.35375 ( 15) hydrogen bonds : bond 0.04195 ( 83) hydrogen bonds : angle 5.97427 ( 228) SS BOND : bond 0.00584 ( 4) SS BOND : angle 1.51146 ( 8) covalent geometry : bond 0.00369 ( 3676) covalent geometry : angle 0.66247 ( 4996) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.435 Fit side-chains REVERT: A 100 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8699 (pt) REVERT: A 128 ILE cc_start: 0.8684 (mp) cc_final: 0.8420 (mp) REVERT: A 202 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8529 (mtpt) REVERT: B 81 MET cc_start: 0.8884 (tmm) cc_final: 0.8578 (ttm) REVERT: B 107 ASN cc_start: 0.8644 (p0) cc_final: 0.8382 (p0) REVERT: L 54 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8084 (tppt) REVERT: L 88 TYR cc_start: 0.9248 (m-80) cc_final: 0.8939 (m-80) REVERT: L 93 ASP cc_start: 0.9345 (t0) cc_final: 0.9085 (t0) outliers start: 16 outliers final: 12 residues processed: 103 average time/residue: 0.1840 time to fit residues: 22.5221 Evaluate side-chains 110 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain L residue 23 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 22 optimal weight: 0.2980 chunk 8 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.101659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.084411 restraints weight = 8912.620| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 4.28 r_work: 0.3165 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3685 Z= 0.198 Angle : 0.742 12.143 5019 Z= 0.373 Chirality : 0.053 0.526 565 Planarity : 0.005 0.051 632 Dihedral : 7.303 59.668 587 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.63 % Allowed : 16.71 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.38 (0.39), residues: 438 helix: None (None), residues: 0 sheet: 0.66 (0.39), residues: 166 loop : -2.10 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 104 HIS 0.004 0.001 HIS B 35 PHE 0.014 0.002 PHE A 86 TYR 0.012 0.002 TYR B 95 ARG 0.011 0.001 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.01106 ( 5) link_NAG-ASN : angle 4.39646 ( 15) hydrogen bonds : bond 0.04631 ( 83) hydrogen bonds : angle 5.98335 ( 228) SS BOND : bond 0.00631 ( 4) SS BOND : angle 1.64095 ( 8) covalent geometry : bond 0.00454 ( 3676) covalent geometry : angle 0.70002 ( 4996) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8691 (mp) cc_final: 0.8415 (mp) REVERT: A 202 LYS cc_start: 0.8926 (mtpt) cc_final: 0.8530 (mtpt) REVERT: B 81 MET cc_start: 0.8880 (tmm) cc_final: 0.8605 (ttm) REVERT: L 54 LYS cc_start: 0.8522 (ttmm) cc_final: 0.8122 (tppt) REVERT: L 88 TYR cc_start: 0.9250 (m-80) cc_final: 0.8951 (m-80) REVERT: L 93 ASP cc_start: 0.9377 (t0) cc_final: 0.9149 (t0) outliers start: 18 outliers final: 14 residues processed: 104 average time/residue: 0.2412 time to fit residues: 29.7495 Evaluate side-chains 113 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 28 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 40 optimal weight: 0.6980 chunk 13 optimal weight: 0.0060 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 0.0170 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.102807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085665 restraints weight = 8824.745| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 4.20 r_work: 0.3184 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3685 Z= 0.150 Angle : 0.717 11.453 5019 Z= 0.359 Chirality : 0.052 0.486 565 Planarity : 0.005 0.051 632 Dihedral : 7.101 59.573 587 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.88 % Allowed : 15.94 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.28 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.72 (0.40), residues: 166 loop : -2.02 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.003 0.001 HIS B 35 PHE 0.010 0.001 PHE B 64 TYR 0.009 0.001 TYR B 95 ARG 0.011 0.001 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.01053 ( 5) link_NAG-ASN : angle 4.19325 ( 15) hydrogen bonds : bond 0.04011 ( 83) hydrogen bonds : angle 5.93437 ( 228) SS BOND : bond 0.00559 ( 4) SS BOND : angle 1.48082 ( 8) covalent geometry : bond 0.00342 ( 3676) covalent geometry : angle 0.67836 ( 4996) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8694 (mp) cc_final: 0.8429 (mp) REVERT: A 202 LYS cc_start: 0.8903 (mtpt) cc_final: 0.8515 (mtpt) REVERT: B 81 MET cc_start: 0.8867 (tmm) cc_final: 0.8474 (ttm) REVERT: L 54 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8096 (tppt) REVERT: L 62 ARG cc_start: 0.7586 (mmt-90) cc_final: 0.6902 (mmp80) REVERT: L 88 TYR cc_start: 0.9243 (m-80) cc_final: 0.8965 (m-80) REVERT: L 93 ASP cc_start: 0.9357 (t0) cc_final: 0.9127 (t0) outliers start: 19 outliers final: 15 residues processed: 107 average time/residue: 0.2411 time to fit residues: 30.9810 Evaluate side-chains 113 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 chunk 33 optimal weight: 0.0980 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 99 ASN B 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.102488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.085134 restraints weight = 8905.597| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 4.29 r_work: 0.3174 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3685 Z= 0.170 Angle : 0.736 11.538 5019 Z= 0.372 Chirality : 0.052 0.503 565 Planarity : 0.005 0.056 632 Dihedral : 7.073 59.701 587 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.63 % Allowed : 16.97 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.38 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.65 (0.39), residues: 173 loop : -2.17 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.002 0.001 HIS B 35 PHE 0.012 0.002 PHE B 64 TYR 0.009 0.001 TYR B 27 ARG 0.013 0.001 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.01048 ( 5) link_NAG-ASN : angle 4.23757 ( 15) hydrogen bonds : bond 0.04266 ( 83) hydrogen bonds : angle 5.88157 ( 228) SS BOND : bond 0.00569 ( 4) SS BOND : angle 1.55002 ( 8) covalent geometry : bond 0.00389 ( 3676) covalent geometry : angle 0.69780 ( 4996) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8695 (mp) cc_final: 0.8429 (mp) REVERT: A 138 ASP cc_start: 0.8884 (m-30) cc_final: 0.8664 (m-30) REVERT: A 202 LYS cc_start: 0.8925 (mtpt) cc_final: 0.8539 (mtpt) REVERT: B 34 MET cc_start: 0.8629 (tpp) cc_final: 0.8096 (mmm) REVERT: B 81 MET cc_start: 0.8869 (tmm) cc_final: 0.8472 (ttm) REVERT: L 54 LYS cc_start: 0.8497 (ttmm) cc_final: 0.8118 (tppt) REVERT: L 88 TYR cc_start: 0.9263 (m-80) cc_final: 0.8992 (m-80) REVERT: L 93 ASP cc_start: 0.9354 (t0) cc_final: 0.9131 (t0) outliers start: 18 outliers final: 15 residues processed: 106 average time/residue: 0.1805 time to fit residues: 22.7853 Evaluate side-chains 113 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 41 optimal weight: 0.0670 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.102772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.085482 restraints weight = 8717.098| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 4.26 r_work: 0.3180 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3685 Z= 0.165 Angle : 0.740 11.327 5019 Z= 0.373 Chirality : 0.052 0.495 565 Planarity : 0.005 0.060 632 Dihedral : 7.030 59.884 587 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.11 % Allowed : 17.74 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.36 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.69 (0.40), residues: 173 loop : -2.17 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.003 0.001 HIS B 35 PHE 0.011 0.002 PHE B 102 TYR 0.009 0.001 TYR B 95 ARG 0.014 0.001 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.01028 ( 5) link_NAG-ASN : angle 4.18112 ( 15) hydrogen bonds : bond 0.04174 ( 83) hydrogen bonds : angle 5.79562 ( 228) SS BOND : bond 0.00557 ( 4) SS BOND : angle 1.54120 ( 8) covalent geometry : bond 0.00377 ( 3676) covalent geometry : angle 0.70261 ( 4996) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8211 (mmm160) cc_final: 0.7614 (tpm170) REVERT: A 128 ILE cc_start: 0.8690 (mp) cc_final: 0.8432 (mp) REVERT: A 138 ASP cc_start: 0.8894 (m-30) cc_final: 0.8670 (m-30) REVERT: A 202 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8551 (mtpt) REVERT: B 34 MET cc_start: 0.8596 (tpp) cc_final: 0.8105 (mmm) REVERT: B 81 MET cc_start: 0.8873 (tmm) cc_final: 0.8470 (ttm) REVERT: L 88 TYR cc_start: 0.9262 (m-80) cc_final: 0.8994 (m-80) REVERT: L 93 ASP cc_start: 0.9349 (t0) cc_final: 0.9118 (t0) outliers start: 16 outliers final: 14 residues processed: 103 average time/residue: 0.2201 time to fit residues: 26.8756 Evaluate side-chains 111 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.0370 chunk 42 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 chunk 5 optimal weight: 0.6980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.102932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.085614 restraints weight = 8756.964| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 4.25 r_work: 0.3181 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3685 Z= 0.163 Angle : 0.757 11.277 5019 Z= 0.379 Chirality : 0.052 0.491 565 Planarity : 0.005 0.057 632 Dihedral : 6.979 59.942 587 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.86 % Allowed : 17.99 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.37 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.73 (0.41), residues: 166 loop : -2.14 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.002 0.000 HIS B 35 PHE 0.012 0.002 PHE B 102 TYR 0.010 0.001 TYR B 95 ARG 0.014 0.001 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.01025 ( 5) link_NAG-ASN : angle 4.16463 ( 15) hydrogen bonds : bond 0.04136 ( 83) hydrogen bonds : angle 5.72559 ( 228) SS BOND : bond 0.00543 ( 4) SS BOND : angle 1.54739 ( 8) covalent geometry : bond 0.00374 ( 3676) covalent geometry : angle 0.72097 ( 4996) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7638 (tpm170) REVERT: A 96 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7855 (mm-30) REVERT: A 128 ILE cc_start: 0.8685 (mp) cc_final: 0.8431 (mp) REVERT: A 138 ASP cc_start: 0.8884 (m-30) cc_final: 0.8666 (m-30) REVERT: A 202 LYS cc_start: 0.8933 (mtpt) cc_final: 0.8561 (mtpt) REVERT: B 34 MET cc_start: 0.8596 (tpp) cc_final: 0.8117 (mmm) REVERT: B 81 MET cc_start: 0.8872 (tmm) cc_final: 0.8481 (ttm) REVERT: L 62 ARG cc_start: 0.7456 (mmt-90) cc_final: 0.6716 (mmp80) REVERT: L 76 ILE cc_start: 0.7943 (tp) cc_final: 0.7656 (tt) REVERT: L 88 TYR cc_start: 0.9262 (m-80) cc_final: 0.8997 (m-80) REVERT: L 93 ASP cc_start: 0.9344 (t0) cc_final: 0.9103 (t0) outliers start: 15 outliers final: 15 residues processed: 105 average time/residue: 0.2707 time to fit residues: 33.7619 Evaluate side-chains 114 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 32 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 26 optimal weight: 0.0980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.085784 restraints weight = 8825.766| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.29 r_work: 0.3183 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3685 Z= 0.157 Angle : 0.751 11.115 5019 Z= 0.378 Chirality : 0.052 0.484 565 Planarity : 0.005 0.052 632 Dihedral : 6.942 59.725 587 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.60 % Allowed : 17.99 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.34 (0.41), residues: 438 helix: None (None), residues: 0 sheet: 0.76 (0.41), residues: 166 loop : -2.12 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.002 0.000 HIS B 35 PHE 0.010 0.001 PHE A 92 TYR 0.009 0.001 TYR A 145 ARG 0.013 0.001 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.01012 ( 5) link_NAG-ASN : angle 4.11337 ( 15) hydrogen bonds : bond 0.04045 ( 83) hydrogen bonds : angle 5.66446 ( 228) SS BOND : bond 0.00529 ( 4) SS BOND : angle 1.49293 ( 8) covalent geometry : bond 0.00359 ( 3676) covalent geometry : angle 0.71610 ( 4996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3263.52 seconds wall clock time: 59 minutes 42.87 seconds (3582.87 seconds total)