Starting phenix.real_space_refine on Thu Jul 24 02:23:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m7b_23709/07_2025/7m7b_23709.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m7b_23709/07_2025/7m7b_23709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m7b_23709/07_2025/7m7b_23709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m7b_23709/07_2025/7m7b_23709.map" model { file = "/net/cci-nas-00/data/ceres_data/7m7b_23709/07_2025/7m7b_23709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m7b_23709/07_2025/7m7b_23709.cif" } resolution = 2.95 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= 0.001 sd= 0.056 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 17 5.16 5 C 3103 2.51 5 N 820 2.21 5 O 958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 4898 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1657 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain: "H" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1622 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 200} Chain: "L" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1591 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 195} 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: 4.25, per 1000 atoms: 0.87 Number of scatterers: 4898 At special positions: 0 Unit cell: (105.692, 91.4418, 104.505, 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 17 16.00 O 958 8.00 N 820 7.00 C 3103 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.02 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " 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 NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 594.7 milliseconds 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 15 sheets defined 12.4% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.570A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.804A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.758A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.833A pdb=" N ASN L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.674A pdb=" N GLU L 86 " --> pdb=" O THR L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 130 Processing helix chain 'L' and resid 185 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.764A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.594A pdb=" N TRP H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.753A pdb=" N ILE H 107 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 126 through 132 removed outlier: 6.800A pdb=" N ALA H 137 " --> pdb=" O PRO H 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 136 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP H 144 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 126 through 132 removed outlier: 6.800A pdb=" N ALA H 137 " --> pdb=" O PRO H 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 136 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP H 144 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 151 through 154 Processing sheet with id=AB2, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.532A pdb=" N ALA L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.532A pdb=" N ALA L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.541A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 149 through 152 203 hydrogen bonds defined for protein. 486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1318 1.33 - 1.46: 990 1.46 - 1.58: 2703 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 5029 Sorted by residual: bond pdb=" CZ ARG A 457 " pdb=" NH2 ARG A 457 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" CZ ARG H 98 " pdb=" NH2 ARG H 98 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.06e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.478 -0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.477 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" CZ ARG A 509 " pdb=" NH2 ARG A 509 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.02e+01 ... (remaining 5024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 4771 1.87 - 3.74: 1779 3.74 - 5.61: 278 5.61 - 7.49: 34 7.49 - 9.36: 1 Bond angle restraints: 6863 Sorted by residual: angle pdb=" CA ASP H 106 " pdb=" CB ASP H 106 " pdb=" CG ASP H 106 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.10e+01 angle pdb=" CA VAL L 163 " pdb=" CB VAL L 163 " pdb=" CG1 VAL L 163 " ideal model delta sigma weight residual 110.40 119.76 -9.36 1.70e+00 3.46e-01 3.03e+01 angle pdb=" N LYS H 143 " pdb=" CA LYS H 143 " pdb=" C LYS H 143 " ideal model delta sigma weight residual 111.69 118.38 -6.69 1.23e+00 6.61e-01 2.96e+01 angle pdb=" CA PHE H 78 " pdb=" CB PHE H 78 " pdb=" CG PHE H 78 " ideal model delta sigma weight residual 113.80 118.81 -5.01 1.00e+00 1.00e+00 2.51e+01 angle pdb=" CB HIS H 53 " pdb=" CG HIS H 53 " pdb=" CD2 HIS H 53 " ideal model delta sigma weight residual 131.20 124.76 6.44 1.30e+00 5.92e-01 2.45e+01 ... (remaining 6858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 2762 17.30 - 34.60: 204 34.60 - 51.90: 28 51.90 - 69.21: 11 69.21 - 86.51: 4 Dihedral angle restraints: 3009 sinusoidal: 1171 harmonic: 1838 Sorted by residual: dihedral pdb=" CA VAL H 142 " pdb=" C VAL H 142 " pdb=" N LYS H 143 " pdb=" CA LYS H 143 " ideal model delta harmonic sigma weight residual -180.00 -150.46 -29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PRO H 185 " pdb=" C PRO H 185 " pdb=" N SER H 186 " pdb=" CA SER H 186 " ideal model delta harmonic sigma weight residual -180.00 -150.77 -29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA VAL L 109 " pdb=" C VAL L 109 " pdb=" N LEU L 110 " pdb=" CA LEU L 110 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 3006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 534 0.104 - 0.207: 191 0.207 - 0.311: 29 0.311 - 0.414: 8 0.414 - 0.518: 2 Chirality restraints: 764 Sorted by residual: chirality pdb=" CA ASN L 173 " pdb=" N ASN L 173 " pdb=" C ASN L 173 " pdb=" CB ASN L 173 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" CA ASN A 370 " pdb=" N ASN A 370 " pdb=" C ASN A 370 " pdb=" CB ASN A 370 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CA SER H 15 " pdb=" N SER H 15 " pdb=" C SER H 15 " pdb=" CB SER H 15 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 761 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 152 " 0.143 2.00e-02 2.50e+03 7.99e-02 1.60e+02 pdb=" CG TRP L 152 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP L 152 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP L 152 " -0.089 2.00e-02 2.50e+03 pdb=" NE1 TRP L 152 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP L 152 " -0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP L 152 " -0.115 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 152 " 0.084 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 152 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP L 152 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 495 " 0.131 2.00e-02 2.50e+03 7.23e-02 1.05e+02 pdb=" CG TYR A 495 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 495 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR A 495 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 495 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR A 495 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR A 495 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 495 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 33 " -0.114 2.00e-02 2.50e+03 6.29e-02 7.91e+01 pdb=" CG TYR L 33 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR L 33 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR L 33 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR L 33 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR L 33 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR L 33 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR L 33 " -0.096 2.00e-02 2.50e+03 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2340 2.99 - 3.47: 4488 3.47 - 3.94: 8045 3.94 - 4.42: 8899 4.42 - 4.90: 15303 Nonbonded interactions: 39075 Sorted by model distance: nonbonded pdb=" N GLU L 51 " pdb=" O GLU L 51 " model vdw 2.512 2.496 nonbonded pdb=" OD2 ASP L 68 " pdb=" OG SER L 71 " model vdw 2.559 3.040 nonbonded pdb=" OD1 ASP L 68 " pdb=" OG SER L 70 " model vdw 2.562 3.040 nonbonded pdb=" OH TYR H 145 " pdb=" OE2 GLU H 148 " model vdw 2.568 3.040 nonbonded pdb=" OE2 GLU L 128 " pdb=" OG1 THR L 135 " model vdw 2.568 3.040 ... (remaining 39070 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: 8.240 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.040 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 0.065 5039 Z= 0.741 Angle : 1.877 9.357 6885 Z= 1.251 Chirality : 0.108 0.518 764 Planarity : 0.015 0.172 881 Dihedral : 13.017 86.508 1813 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.85 % Peptide Plane: Cis-proline : 7.32 % 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: -0.73 (0.32), residues: 629 helix: -3.61 (0.50), residues: 41 sheet: 0.44 (0.37), residues: 200 loop : -0.61 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.143 0.019 TRP L 152 HIS 0.011 0.004 HIS H 164 PHE 0.074 0.014 PHE H 29 TYR 0.131 0.021 TYR A 495 ARG 0.008 0.001 ARG L 55 Details of bonding type rmsd link_NAG-ASN : bond 0.01155 ( 2) link_NAG-ASN : angle 4.42540 ( 6) hydrogen bonds : bond 0.14397 ( 181) hydrogen bonds : angle 8.85591 ( 486) SS BOND : bond 0.01119 ( 8) SS BOND : angle 1.53725 ( 16) covalent geometry : bond 0.01241 ( 5029) covalent geometry : angle 1.87442 ( 6863) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7689 (p0) cc_final: 0.7397 (p0) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 1.4783 time to fit residues: 58.4964 Evaluate side-chains 21 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 437 ASN ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.054593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.039460 restraints weight = 21581.175| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.44 r_work: 0.2754 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5039 Z= 0.129 Angle : 0.628 5.430 6885 Z= 0.346 Chirality : 0.047 0.185 764 Planarity : 0.005 0.042 881 Dihedral : 6.182 24.449 727 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.55 % Allowed : 5.69 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.25 (0.32), residues: 629 helix: -2.68 (0.71), residues: 41 sheet: 0.51 (0.34), residues: 218 loop : -0.22 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 152 HIS 0.002 0.001 HIS H 53 PHE 0.019 0.001 PHE H 78 TYR 0.025 0.001 TYR A 369 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 2) link_NAG-ASN : angle 1.87059 ( 6) hydrogen bonds : bond 0.03761 ( 181) hydrogen bonds : angle 6.34267 ( 486) SS BOND : bond 0.00344 ( 8) SS BOND : angle 0.58754 ( 16) covalent geometry : bond 0.00275 ( 5029) covalent geometry : angle 0.62578 ( 6863) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.9385 (p0) cc_final: 0.9118 (p0) REVERT: L 84 GLU cc_start: 0.9032 (pm20) cc_final: 0.8608 (pm20) REVERT: L 85 ASP cc_start: 0.8026 (m-30) cc_final: 0.7772 (m-30) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 2.4829 time to fit residues: 72.8556 Evaluate side-chains 21 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 156 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN H 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.054543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.039367 restraints weight = 21469.896| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.39 r_work: 0.2758 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5039 Z= 0.125 Angle : 0.562 5.882 6885 Z= 0.306 Chirality : 0.046 0.181 764 Planarity : 0.005 0.047 881 Dihedral : 5.385 21.918 727 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.37 % Allowed : 7.16 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.33), residues: 629 helix: -2.87 (0.62), residues: 41 sheet: 0.63 (0.35), residues: 226 loop : -0.04 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 189 HIS 0.002 0.001 HIS L 192 PHE 0.013 0.001 PHE H 78 TYR 0.022 0.001 TYR A 369 ARG 0.011 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 2) link_NAG-ASN : angle 1.65972 ( 6) hydrogen bonds : bond 0.03473 ( 181) hydrogen bonds : angle 5.78973 ( 486) SS BOND : bond 0.00279 ( 8) SS BOND : angle 0.56296 ( 16) covalent geometry : bond 0.00282 ( 5029) covalent geometry : angle 0.56018 ( 6863) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.9357 (p0) cc_final: 0.9075 (p0) REVERT: A 516 GLU cc_start: 0.8740 (pt0) cc_final: 0.8212 (pm20) REVERT: L 84 GLU cc_start: 0.8974 (pm20) cc_final: 0.8750 (pm20) REVERT: L 85 ASP cc_start: 0.8027 (m-30) cc_final: 0.7484 (m-30) outliers start: 2 outliers final: 1 residues processed: 27 average time/residue: 2.0563 time to fit residues: 59.2074 Evaluate side-chains 20 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 0.0070 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.0170 chunk 30 optimal weight: 0.5980 overall best weight: 1.3240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.053449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.038618 restraints weight = 21826.271| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.27 r_work: 0.2733 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5039 Z= 0.158 Angle : 0.557 7.972 6885 Z= 0.300 Chirality : 0.045 0.178 764 Planarity : 0.005 0.042 881 Dihedral : 5.245 22.753 727 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.92 % Allowed : 8.26 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.33), residues: 629 helix: -2.50 (0.70), residues: 41 sheet: 0.63 (0.35), residues: 228 loop : -0.08 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS L 192 PHE 0.012 0.001 PHE H 78 TYR 0.021 0.001 TYR A 369 ARG 0.003 0.000 ARG H 210 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 2) link_NAG-ASN : angle 1.53200 ( 6) hydrogen bonds : bond 0.03412 ( 181) hydrogen bonds : angle 5.83868 ( 486) SS BOND : bond 0.00237 ( 8) SS BOND : angle 0.58361 ( 16) covalent geometry : bond 0.00366 ( 5029) covalent geometry : angle 0.55513 ( 6863) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.9058 (t0) cc_final: 0.8838 (t0) REVERT: A 428 ASP cc_start: 0.9330 (p0) cc_final: 0.9028 (p0) REVERT: L 85 ASP cc_start: 0.8086 (m-30) cc_final: 0.7543 (m-30) REVERT: L 164 GLU cc_start: 0.7167 (pm20) cc_final: 0.6916 (pt0) outliers start: 5 outliers final: 1 residues processed: 23 average time/residue: 1.9964 time to fit residues: 48.9368 Evaluate side-chains 18 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 201 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.053891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.038928 restraints weight = 21756.796| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.28 r_work: 0.2745 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5039 Z= 0.120 Angle : 0.543 8.474 6885 Z= 0.289 Chirality : 0.045 0.168 764 Planarity : 0.005 0.039 881 Dihedral : 4.948 22.475 727 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.55 % Allowed : 10.28 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.07 (0.33), residues: 629 helix: -2.65 (0.64), residues: 40 sheet: 0.63 (0.35), residues: 229 loop : -0.10 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 100 HIS 0.003 0.001 HIS L 201 PHE 0.011 0.001 PHE H 78 TYR 0.021 0.001 TYR A 369 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00015 ( 2) link_NAG-ASN : angle 1.55042 ( 6) hydrogen bonds : bond 0.03316 ( 181) hydrogen bonds : angle 5.63664 ( 486) SS BOND : bond 0.00224 ( 8) SS BOND : angle 0.47369 ( 16) covalent geometry : bond 0.00277 ( 5029) covalent geometry : angle 0.54147 ( 6863) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.9043 (t0) cc_final: 0.8803 (t0) REVERT: A 428 ASP cc_start: 0.9322 (p0) cc_final: 0.9010 (p0) REVERT: L 85 ASP cc_start: 0.8102 (m-30) cc_final: 0.7822 (m-30) REVERT: L 86 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8100 (mt-10) outliers start: 3 outliers final: 0 residues processed: 26 average time/residue: 1.7138 time to fit residues: 46.8063 Evaluate side-chains 20 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 19 optimal weight: 0.0070 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 1 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.054069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.039186 restraints weight = 21479.488| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.28 r_work: 0.2757 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5039 Z= 0.105 Angle : 0.517 10.097 6885 Z= 0.273 Chirality : 0.044 0.165 764 Planarity : 0.004 0.037 881 Dihedral : 4.632 21.303 727 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.55 % Allowed : 11.74 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.10 (0.34), residues: 629 helix: -2.63 (0.72), residues: 34 sheet: 0.83 (0.36), residues: 221 loop : -0.07 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 100 HIS 0.003 0.001 HIS L 201 PHE 0.010 0.001 PHE H 78 TYR 0.021 0.001 TYR A 369 ARG 0.001 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 2) link_NAG-ASN : angle 1.38298 ( 6) hydrogen bonds : bond 0.03119 ( 181) hydrogen bonds : angle 5.45855 ( 486) SS BOND : bond 0.00205 ( 8) SS BOND : angle 0.48093 ( 16) covalent geometry : bond 0.00240 ( 5029) covalent geometry : angle 0.51618 ( 6863) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8909 (mp0) REVERT: A 405 ASP cc_start: 0.8997 (t0) cc_final: 0.8756 (t0) REVERT: A 428 ASP cc_start: 0.9351 (p0) cc_final: 0.9060 (p0) REVERT: A 516 GLU cc_start: 0.8804 (pt0) cc_final: 0.8345 (pm20) REVERT: L 86 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7966 (mt-10) REVERT: L 164 GLU cc_start: 0.7178 (pm20) cc_final: 0.6508 (pt0) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 1.6570 time to fit residues: 47.2189 Evaluate side-chains 20 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.053604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.038636 restraints weight = 21469.784| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.35 r_work: 0.2737 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5039 Z= 0.140 Angle : 0.533 9.900 6885 Z= 0.282 Chirality : 0.045 0.167 764 Planarity : 0.005 0.037 881 Dihedral : 4.713 22.141 727 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.73 % Allowed : 12.11 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.34), residues: 629 helix: -2.41 (0.74), residues: 34 sheet: 0.80 (0.35), residues: 229 loop : -0.09 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 100 HIS 0.002 0.001 HIS L 192 PHE 0.011 0.001 PHE H 78 TYR 0.021 0.001 TYR A 369 ARG 0.003 0.000 ARG H 210 Details of bonding type rmsd link_NAG-ASN : bond 0.00053 ( 2) link_NAG-ASN : angle 1.44000 ( 6) hydrogen bonds : bond 0.03254 ( 181) hydrogen bonds : angle 5.53165 ( 486) SS BOND : bond 0.00252 ( 8) SS BOND : angle 0.52588 ( 16) covalent geometry : bond 0.00323 ( 5029) covalent geometry : angle 0.53173 ( 6863) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.9034 (t0) cc_final: 0.8798 (t0) REVERT: A 428 ASP cc_start: 0.9343 (p0) cc_final: 0.9030 (p0) REVERT: L 86 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8048 (mt-10) outliers start: 4 outliers final: 1 residues processed: 24 average time/residue: 1.7459 time to fit residues: 44.5158 Evaluate side-chains 21 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 0.0170 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.054222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.039363 restraints weight = 21557.649| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.28 r_work: 0.2759 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5039 Z= 0.107 Angle : 0.529 12.174 6885 Z= 0.276 Chirality : 0.044 0.162 764 Planarity : 0.004 0.037 881 Dihedral : 4.501 22.794 727 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.37 % Allowed : 13.03 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.34), residues: 629 helix: -2.36 (0.77), residues: 34 sheet: 0.96 (0.36), residues: 223 loop : 0.01 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 100 HIS 0.002 0.000 HIS L 201 PHE 0.010 0.001 PHE H 78 TYR 0.020 0.001 TYR A 369 ARG 0.003 0.000 ARG H 210 Details of bonding type rmsd link_NAG-ASN : bond 0.00010 ( 2) link_NAG-ASN : angle 1.47735 ( 6) hydrogen bonds : bond 0.03035 ( 181) hydrogen bonds : angle 5.37177 ( 486) SS BOND : bond 0.00228 ( 8) SS BOND : angle 0.44801 ( 16) covalent geometry : bond 0.00246 ( 5029) covalent geometry : angle 0.52722 ( 6863) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.606 Fit side-chains REVERT: A 405 ASP cc_start: 0.9009 (t0) cc_final: 0.8771 (t0) REVERT: A 428 ASP cc_start: 0.9348 (p0) cc_final: 0.9032 (p0) REVERT: L 86 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7992 (mt-10) REVERT: L 114 LYS cc_start: 0.8825 (mttm) cc_final: 0.8453 (tptt) REVERT: L 153 LYS cc_start: 0.9174 (ttpp) cc_final: 0.8503 (tppt) outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 1.5120 time to fit residues: 44.3087 Evaluate side-chains 24 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 45 optimal weight: 0.0370 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 1 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.054140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.039118 restraints weight = 21302.266| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.27 r_work: 0.2753 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5039 Z= 0.114 Angle : 0.528 11.831 6885 Z= 0.274 Chirality : 0.044 0.165 764 Planarity : 0.004 0.036 881 Dihedral : 4.468 22.377 727 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.37 % Allowed : 13.94 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.28 (0.34), residues: 629 helix: -2.29 (0.80), residues: 34 sheet: 1.00 (0.36), residues: 224 loop : -0.03 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 189 HIS 0.001 0.000 HIS L 201 PHE 0.010 0.001 PHE H 78 TYR 0.021 0.001 TYR A 369 ARG 0.002 0.000 ARG H 210 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 2) link_NAG-ASN : angle 1.38756 ( 6) hydrogen bonds : bond 0.03040 ( 181) hydrogen bonds : angle 5.39894 ( 486) SS BOND : bond 0.00220 ( 8) SS BOND : angle 0.47823 ( 16) covalent geometry : bond 0.00265 ( 5029) covalent geometry : angle 0.52634 ( 6863) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.801 Fit side-chains REVERT: A 405 ASP cc_start: 0.9000 (t0) cc_final: 0.8756 (t0) REVERT: A 428 ASP cc_start: 0.9331 (p0) cc_final: 0.9003 (p0) REVERT: L 86 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8046 (mt-10) REVERT: L 114 LYS cc_start: 0.8826 (mttm) cc_final: 0.8424 (tptt) REVERT: L 153 LYS cc_start: 0.9175 (ttpp) cc_final: 0.8504 (tppt) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 1.8679 time to fit residues: 47.0537 Evaluate side-chains 23 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.0670 chunk 57 optimal weight: 0.0970 chunk 27 optimal weight: 0.0270 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.054847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.039893 restraints weight = 21445.781| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.27 r_work: 0.2783 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5039 Z= 0.093 Angle : 0.527 12.460 6885 Z= 0.274 Chirality : 0.044 0.161 764 Planarity : 0.004 0.036 881 Dihedral : 4.249 21.566 727 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.18 % Allowed : 14.13 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.35), residues: 629 helix: -2.26 (0.81), residues: 34 sheet: 1.05 (0.36), residues: 224 loop : 0.04 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 189 HIS 0.001 0.000 HIS L 201 PHE 0.009 0.001 PHE H 78 TYR 0.020 0.001 TYR A 369 ARG 0.002 0.000 ARG A 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 2) link_NAG-ASN : angle 1.38338 ( 6) hydrogen bonds : bond 0.02820 ( 181) hydrogen bonds : angle 5.23733 ( 486) SS BOND : bond 0.00227 ( 8) SS BOND : angle 0.45106 ( 16) covalent geometry : bond 0.00213 ( 5029) covalent geometry : angle 0.52589 ( 6863) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.642 Fit side-chains REVERT: A 405 ASP cc_start: 0.8909 (t0) cc_final: 0.8672 (t0) REVERT: A 428 ASP cc_start: 0.9318 (p0) cc_final: 0.8985 (p0) REVERT: L 86 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8021 (mt-10) REVERT: L 114 LYS cc_start: 0.8833 (mttm) cc_final: 0.8407 (tptt) REVERT: L 153 LYS cc_start: 0.9190 (ttpp) cc_final: 0.8513 (tppt) outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 2.1338 time to fit residues: 54.0680 Evaluate side-chains 23 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 1 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.052062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.037256 restraints weight = 21749.215| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.25 r_work: 0.2688 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5039 Z= 0.280 Angle : 0.622 12.125 6885 Z= 0.327 Chirality : 0.046 0.171 764 Planarity : 0.005 0.037 881 Dihedral : 5.208 24.890 727 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.18 % Allowed : 14.68 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.12 (0.34), residues: 629 helix: -2.21 (0.71), residues: 41 sheet: 0.88 (0.36), residues: 227 loop : -0.10 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 189 HIS 0.003 0.001 HIS L 192 PHE 0.011 0.002 PHE H 78 TYR 0.021 0.002 TYR A 369 ARG 0.006 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 2) link_NAG-ASN : angle 1.56753 ( 6) hydrogen bonds : bond 0.03812 ( 181) hydrogen bonds : angle 5.86088 ( 486) SS BOND : bond 0.00327 ( 8) SS BOND : angle 0.81848 ( 16) covalent geometry : bond 0.00645 ( 5029) covalent geometry : angle 0.61975 ( 6863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6477.21 seconds wall clock time: 122 minutes 17.63 seconds (7337.63 seconds total)