Starting phenix.real_space_refine on Wed Jul 23 23:38:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bt2_44880/07_2025/9bt2_44880_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bt2_44880/07_2025/9bt2_44880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bt2_44880/07_2025/9bt2_44880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bt2_44880/07_2025/9bt2_44880.map" model { file = "/net/cci-nas-00/data/ceres_data/9bt2_44880/07_2025/9bt2_44880_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bt2_44880/07_2025/9bt2_44880_trim.cif" } resolution = 1.93 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= -0.002 sd= 0.063 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: 5 Type Number sf(0) Gaussians S 8 5.16 5 C 1518 2.51 5 N 355 2.21 5 O 470 1.98 5 H 2106 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 4457 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 4298 Classifications: {'peptide': 268} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 258} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 4.55, per 1000 atoms: 1.02 Number of scatterers: 4457 At special positions: 0 Unit cell: (67.4182, 59.328, 76.4073, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 470 8.00 N 355 7.00 C 1518 6.00 H 2106 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.05 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1401 " - " ASN A 19 " " NAG A1402 " - " ASN A 58 " " NAG A1403 " - " ASN A 171 " " NAG A1404 " - " ASN A 192 " " NAG A1405 " - " ASN A 251 " " NAG B 1 " - " ASN A 132 " " NAG C 1 " - " ASN A 188 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 301.9 milliseconds 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 508 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 6 sheets defined 1.5% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.729A pdb=" N GLN A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 39 removed outlier: 8.207A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY A 101 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 68 removed outlier: 3.624A pdb=" N ASN A 278 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 80 through 81 removed outlier: 8.017A pdb=" N THR A 241 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N TRP A 174 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA6, first strand: chain 'A' and resid 109 through 113 73 hydrogen bonds defined for protein. 192 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: 1.51 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 2106 1.13 - 1.30: 351 1.30 - 1.47: 1014 1.47 - 1.64: 1040 1.64 - 1.81: 10 Bond restraints: 4521 Sorted by residual: bond pdb=" NE2 GLN A 140 " pdb="HE22 GLN A 140 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE2 GLN A 152 " pdb="HE22 GLN A 152 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLU A 172 " pdb=" H GLU A 172 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ASP A 271 " pdb=" H ASP A 271 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" NE2 GLN A 255 " pdb="HE22 GLN A 255 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 4516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6111 1.64 - 3.28: 1208 3.28 - 4.92: 419 4.92 - 6.56: 248 6.56 - 8.20: 45 Bond angle restraints: 8031 Sorted by residual: angle pdb=" CB HIS A 234 " pdb=" CG HIS A 234 " pdb=" CD2 HIS A 234 " ideal model delta sigma weight residual 131.20 124.38 6.82 1.30e+00 5.92e-01 2.75e+01 angle pdb=" CA THR A 154 " pdb=" CB THR A 154 " pdb=" CG2 THR A 154 " ideal model delta sigma weight residual 110.50 118.70 -8.20 1.70e+00 3.46e-01 2.33e+01 angle pdb=" CB HIS A 201 " pdb=" CG HIS A 201 " pdb=" CD2 HIS A 201 " ideal model delta sigma weight residual 131.20 125.44 5.76 1.30e+00 5.92e-01 1.96e+01 angle pdb=" OE1 GLN A 152 " pdb=" CD GLN A 152 " pdb=" NE2 GLN A 152 " ideal model delta sigma weight residual 122.60 118.49 4.11 1.00e+00 1.00e+00 1.69e+01 angle pdb=" OD1 ASN A 73 " pdb=" CG ASN A 73 " pdb=" ND2 ASN A 73 " ideal model delta sigma weight residual 122.60 118.55 4.05 1.00e+00 1.00e+00 1.64e+01 ... (remaining 8026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.99: 2149 19.99 - 39.99: 110 39.99 - 59.98: 56 59.98 - 79.98: 27 79.98 - 99.97: 6 Dihedral angle restraints: 2348 sinusoidal: 1319 harmonic: 1029 Sorted by residual: dihedral pdb=" CA ASN A 73 " pdb=" C ASN A 73 " pdb=" N PHE A 74 " pdb=" CA PHE A 74 " ideal model delta harmonic sigma weight residual 180.00 150.75 29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA TYR A 266 " pdb=" C TYR A 266 " pdb=" N LEU A 267 " pdb=" CA LEU A 267 " ideal model delta harmonic sigma weight residual 180.00 153.40 26.60 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA PHE A 200 " pdb=" C PHE A 200 " pdb=" N HIS A 201 " pdb=" CA HIS A 201 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 2345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 163 0.063 - 0.125: 134 0.125 - 0.188: 85 0.188 - 0.251: 16 0.251 - 0.313: 3 Chirality restraints: 401 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.85e+01 chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.25e+01 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.13e+01 ... (remaining 398 not shown) Planarity restraints: 657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 132 " 0.183 2.00e-02 2.50e+03 1.37e-01 2.81e+02 pdb=" CG ASN A 132 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 132 " -0.117 2.00e-02 2.50e+03 pdb=" ND2 ASN A 132 " -0.031 2.00e-02 2.50e+03 pdb="HD21 ASN A 132 " -0.166 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 197 " -0.169 2.00e-02 2.50e+03 5.57e-02 1.24e+02 pdb=" CG TRP A 197 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP A 197 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP A 197 " 0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP A 197 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP A 197 " 0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP A 197 " 0.034 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 197 " -0.037 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 197 " 0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP A 197 " -0.027 2.00e-02 2.50e+03 pdb=" HD1 TRP A 197 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP A 197 " 0.036 2.00e-02 2.50e+03 pdb=" HE3 TRP A 197 " 0.058 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 197 " -0.063 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 197 " 0.033 2.00e-02 2.50e+03 pdb=" HH2 TRP A 197 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 256 " 0.121 2.00e-02 2.50e+03 6.35e-02 1.21e+02 pdb=" CG TYR A 256 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 256 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 256 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 256 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 256 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 256 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 256 " 0.141 2.00e-02 2.50e+03 pdb=" HD1 TYR A 256 " -0.063 2.00e-02 2.50e+03 pdb=" HD2 TYR A 256 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 TYR A 256 " -0.035 2.00e-02 2.50e+03 pdb=" HE2 TYR A 256 " -0.075 2.00e-02 2.50e+03 ... (remaining 654 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 413 2.20 - 2.80: 7968 2.80 - 3.40: 11890 3.40 - 4.00: 17472 4.00 - 4.60: 24760 Nonbonded interactions: 62503 Sorted by model distance: nonbonded pdb=" HG SER A 128 " pdb=" H VAL A 129 " model vdw 1.606 2.100 nonbonded pdb=" OD1 ASN A 108 " pdb=" HG SER A 119 " model vdw 1.609 2.450 nonbonded pdb=" H ASP A 250 " pdb=" H ASN A 251 " model vdw 1.685 2.100 nonbonded pdb=" HH TYR A 66 " pdb=" OE2 GLU A 205 " model vdw 1.695 2.450 nonbonded pdb=" OE2 GLU A 120 " pdb=" HG SER A 165 " model vdw 1.717 2.450 ... (remaining 62498 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: 5.980 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: 0.080 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.690 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 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 : 0.015 0.073 2430 Z= 0.805 Angle : 1.693 8.204 3334 Z= 1.061 Chirality : 0.105 0.313 401 Planarity : 0.014 0.114 392 Dihedral : 14.056 99.973 1031 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.40 % Allowed : 0.00 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.61 (0.48), residues: 266 helix: None (None), residues: 0 sheet: 0.11 (0.48), residues: 96 loop : -0.71 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.115 0.021 TRP A 197 HIS 0.006 0.003 HIS A 160 PHE 0.070 0.014 PHE A 74 TYR 0.113 0.019 TYR A 256 ARG 0.008 0.001 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.01043 ( 7) link_NAG-ASN : angle 4.33832 ( 21) link_ALPHA1-6 : bond 0.02349 ( 1) link_ALPHA1-6 : angle 2.97146 ( 3) link_BETA1-4 : bond 0.01736 ( 3) link_BETA1-4 : angle 4.18942 ( 9) link_ALPHA1-3 : bond 0.02443 ( 1) link_ALPHA1-3 : angle 2.55948 ( 3) hydrogen bonds : bond 0.13609 ( 73) hydrogen bonds : angle 8.04005 ( 192) SS BOND : bond 0.01132 ( 3) SS BOND : angle 2.07968 ( 6) covalent geometry : bond 0.01468 ( 2415) covalent geometry : angle 1.64753 ( 3292) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.356 Fit side-chains REVERT: A 54 ARG cc_start: 0.9209 (mtt180) cc_final: 0.6993 (mmt90) REVERT: A 187 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8548 (mmtm) REVERT: A 206 ARG cc_start: 0.8948 (mtm-85) cc_final: 0.7273 (mmt-90) outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 3.2607 time to fit residues: 126.0291 Evaluate side-chains 21 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.077241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.061590 restraints weight = 9398.880| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.01 r_work: 0.2701 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9195 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 2430 Z= 0.237 Angle : 0.842 15.311 3334 Z= 0.427 Chirality : 0.048 0.307 401 Planarity : 0.004 0.027 392 Dihedral : 11.574 76.460 547 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.62 % Allowed : 5.67 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.27 (0.49), residues: 98 loop : -0.35 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 174 HIS 0.004 0.002 HIS A 160 PHE 0.019 0.002 PHE A 74 TYR 0.014 0.002 TYR A 50 ARG 0.002 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 7) link_NAG-ASN : angle 2.17510 ( 21) link_ALPHA1-6 : bond 0.00717 ( 1) link_ALPHA1-6 : angle 1.83411 ( 3) link_BETA1-4 : bond 0.00182 ( 3) link_BETA1-4 : angle 2.38292 ( 9) link_ALPHA1-3 : bond 0.00983 ( 1) link_ALPHA1-3 : angle 2.26887 ( 3) hydrogen bonds : bond 0.05520 ( 73) hydrogen bonds : angle 7.68469 ( 192) SS BOND : bond 0.01255 ( 3) SS BOND : angle 5.21267 ( 6) covalent geometry : bond 0.00579 ( 2415) covalent geometry : angle 0.78446 ( 3292) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.354 Fit side-chains REVERT: A 54 ARG cc_start: 0.9178 (mtt180) cc_final: 0.6827 (mmt90) REVERT: A 187 LYS cc_start: 0.8765 (mtpt) cc_final: 0.8493 (mptp) REVERT: A 206 ARG cc_start: 0.9063 (mtm-85) cc_final: 0.7617 (mtp180) outliers start: 4 outliers final: 2 residues processed: 23 average time/residue: 3.4451 time to fit residues: 80.7144 Evaluate side-chains 21 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.077965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.062738 restraints weight = 9652.095| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.01 r_work: 0.2728 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 2430 Z= 0.160 Angle : 0.693 11.801 3334 Z= 0.358 Chirality : 0.046 0.260 401 Planarity : 0.004 0.031 392 Dihedral : 10.196 65.407 547 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.81 % Allowed : 6.48 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.09 (0.51), residues: 97 loop : -0.30 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 174 HIS 0.003 0.001 HIS A 160 PHE 0.018 0.002 PHE A 74 TYR 0.011 0.001 TYR A 50 ARG 0.003 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 7) link_NAG-ASN : angle 1.73807 ( 21) link_ALPHA1-6 : bond 0.00673 ( 1) link_ALPHA1-6 : angle 1.81304 ( 3) link_BETA1-4 : bond 0.00243 ( 3) link_BETA1-4 : angle 1.58479 ( 9) link_ALPHA1-3 : bond 0.01138 ( 1) link_ALPHA1-3 : angle 1.54469 ( 3) hydrogen bonds : bond 0.04597 ( 73) hydrogen bonds : angle 7.35782 ( 192) SS BOND : bond 0.00785 ( 3) SS BOND : angle 3.27844 ( 6) covalent geometry : bond 0.00354 ( 2415) covalent geometry : angle 0.65989 ( 3292) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.375 Fit side-chains REVERT: A 26 ASN cc_start: 0.8440 (m-40) cc_final: 0.8134 (t0) REVERT: A 54 ARG cc_start: 0.9117 (mtt180) cc_final: 0.6681 (mmt90) REVERT: A 187 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8350 (mptp) REVERT: A 206 ARG cc_start: 0.9059 (mtm-85) cc_final: 0.7562 (mtp180) outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 3.2272 time to fit residues: 69.2152 Evaluate side-chains 21 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 14 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 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 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.077422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.061960 restraints weight = 9511.342| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.02 r_work: 0.2713 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2430 Z= 0.188 Angle : 0.676 10.073 3334 Z= 0.345 Chirality : 0.046 0.226 401 Planarity : 0.003 0.030 392 Dihedral : 8.975 54.263 547 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.81 % Allowed : 6.48 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.06 (0.51), residues: 98 loop : -0.27 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 174 HIS 0.003 0.001 HIS A 234 PHE 0.018 0.002 PHE A 74 TYR 0.013 0.002 TYR A 50 ARG 0.002 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 7) link_NAG-ASN : angle 1.76695 ( 21) link_ALPHA1-6 : bond 0.00767 ( 1) link_ALPHA1-6 : angle 1.84792 ( 3) link_BETA1-4 : bond 0.00314 ( 3) link_BETA1-4 : angle 1.70824 ( 9) link_ALPHA1-3 : bond 0.00970 ( 1) link_ALPHA1-3 : angle 1.91383 ( 3) hydrogen bonds : bond 0.04442 ( 73) hydrogen bonds : angle 7.25566 ( 192) SS BOND : bond 0.00643 ( 3) SS BOND : angle 2.97875 ( 6) covalent geometry : bond 0.00417 ( 2415) covalent geometry : angle 0.64170 ( 3292) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.380 Fit side-chains REVERT: A 54 ARG cc_start: 0.9174 (mtt180) cc_final: 0.6693 (mmt90) REVERT: A 187 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8300 (mptp) REVERT: A 206 ARG cc_start: 0.9079 (mtm-85) cc_final: 0.7534 (mtp180) outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 3.5940 time to fit residues: 84.4154 Evaluate side-chains 22 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 11 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.077909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.062506 restraints weight = 9622.152| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.02 r_work: 0.2717 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9186 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2430 Z= 0.179 Angle : 0.649 9.056 3334 Z= 0.333 Chirality : 0.046 0.222 401 Planarity : 0.003 0.029 392 Dihedral : 8.473 52.701 547 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.81 % Allowed : 6.88 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.30 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.04 (0.50), residues: 98 loop : -0.29 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 174 HIS 0.003 0.001 HIS A 201 PHE 0.015 0.002 PHE A 74 TYR 0.011 0.002 TYR A 50 ARG 0.001 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 7) link_NAG-ASN : angle 1.69423 ( 21) link_ALPHA1-6 : bond 0.00866 ( 1) link_ALPHA1-6 : angle 1.87435 ( 3) link_BETA1-4 : bond 0.00274 ( 3) link_BETA1-4 : angle 1.57644 ( 9) link_ALPHA1-3 : bond 0.00957 ( 1) link_ALPHA1-3 : angle 1.67680 ( 3) hydrogen bonds : bond 0.04369 ( 73) hydrogen bonds : angle 7.21846 ( 192) SS BOND : bond 0.00590 ( 3) SS BOND : angle 2.71059 ( 6) covalent geometry : bond 0.00391 ( 2415) covalent geometry : angle 0.61884 ( 3292) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.334 Fit side-chains REVERT: A 54 ARG cc_start: 0.9184 (mtt180) cc_final: 0.6769 (mmt90) REVERT: A 187 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8390 (mptp) REVERT: A 206 ARG cc_start: 0.9095 (mtm-85) cc_final: 0.7627 (mtp180) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 3.3240 time to fit residues: 74.7828 Evaluate side-chains 22 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 chunk 2 optimal weight: 0.3980 chunk 8 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.0870 chunk 16 optimal weight: 0.3980 chunk 15 optimal weight: 0.2980 overall best weight: 0.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.080863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.065604 restraints weight = 9368.520| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.03 r_work: 0.2780 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2430 Z= 0.113 Angle : 0.582 6.828 3334 Z= 0.300 Chirality : 0.045 0.227 401 Planarity : 0.003 0.029 392 Dihedral : 7.729 52.566 547 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.21 % Allowed : 6.48 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.15 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.37 (0.49), residues: 100 loop : -0.36 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 PHE 0.014 0.001 PHE A 74 TYR 0.009 0.001 TYR A 212 ARG 0.001 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 7) link_NAG-ASN : angle 1.44141 ( 21) link_ALPHA1-6 : bond 0.00756 ( 1) link_ALPHA1-6 : angle 1.78735 ( 3) link_BETA1-4 : bond 0.00215 ( 3) link_BETA1-4 : angle 1.37070 ( 9) link_ALPHA1-3 : bond 0.01119 ( 1) link_ALPHA1-3 : angle 1.63116 ( 3) hydrogen bonds : bond 0.03624 ( 73) hydrogen bonds : angle 7.00888 ( 192) SS BOND : bond 0.00348 ( 3) SS BOND : angle 2.02839 ( 6) covalent geometry : bond 0.00243 ( 2415) covalent geometry : angle 0.55871 ( 3292) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.375 Fit side-chains REVERT: A 54 ARG cc_start: 0.9102 (mtt180) cc_final: 0.6713 (mmt90) REVERT: A 115 LYS cc_start: 0.8892 (mtmm) cc_final: 0.8667 (mttp) REVERT: A 187 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8322 (mptp) REVERT: A 206 ARG cc_start: 0.9072 (mtm-85) cc_final: 0.7591 (mtp180) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 3.4224 time to fit residues: 80.2110 Evaluate side-chains 23 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 25 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.078509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.063350 restraints weight = 9674.632| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.02 r_work: 0.2743 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2430 Z= 0.169 Angle : 0.611 7.390 3334 Z= 0.313 Chirality : 0.045 0.218 401 Planarity : 0.003 0.028 392 Dihedral : 7.665 53.275 547 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.21 % Allowed : 6.88 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.06 (0.50), residues: 98 loop : -0.27 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 174 HIS 0.003 0.001 HIS A 201 PHE 0.014 0.001 PHE A 74 TYR 0.011 0.001 TYR A 50 ARG 0.001 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 7) link_NAG-ASN : angle 1.62658 ( 21) link_ALPHA1-6 : bond 0.00885 ( 1) link_ALPHA1-6 : angle 1.80089 ( 3) link_BETA1-4 : bond 0.00301 ( 3) link_BETA1-4 : angle 1.61159 ( 9) link_ALPHA1-3 : bond 0.00887 ( 1) link_ALPHA1-3 : angle 1.77000 ( 3) hydrogen bonds : bond 0.04085 ( 73) hydrogen bonds : angle 7.04675 ( 192) SS BOND : bond 0.00498 ( 3) SS BOND : angle 2.25426 ( 6) covalent geometry : bond 0.00371 ( 2415) covalent geometry : angle 0.58262 ( 3292) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.348 Fit side-chains REVERT: A 54 ARG cc_start: 0.9147 (mtt180) cc_final: 0.6675 (mmt90) REVERT: A 115 LYS cc_start: 0.8908 (mtmm) cc_final: 0.8686 (mttp) REVERT: A 187 LYS cc_start: 0.8699 (mtpt) cc_final: 0.8313 (mptp) REVERT: A 206 ARG cc_start: 0.9084 (mtm-85) cc_final: 0.7544 (mtp180) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 3.4742 time to fit residues: 81.4391 Evaluate side-chains 24 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.078328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.062807 restraints weight = 9451.332| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.02 r_work: 0.2723 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9189 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2430 Z= 0.183 Angle : 0.630 7.790 3334 Z= 0.324 Chirality : 0.045 0.214 401 Planarity : 0.003 0.027 392 Dihedral : 7.599 53.231 547 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.62 % Allowed : 6.48 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.07 (0.50), residues: 98 loop : -0.29 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 174 HIS 0.002 0.001 HIS A 160 PHE 0.014 0.002 PHE A 121 TYR 0.011 0.002 TYR A 50 ARG 0.001 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 7) link_NAG-ASN : angle 1.66314 ( 21) link_ALPHA1-6 : bond 0.00963 ( 1) link_ALPHA1-6 : angle 1.82893 ( 3) link_BETA1-4 : bond 0.00287 ( 3) link_BETA1-4 : angle 1.60238 ( 9) link_ALPHA1-3 : bond 0.00837 ( 1) link_ALPHA1-3 : angle 1.62884 ( 3) hydrogen bonds : bond 0.04203 ( 73) hydrogen bonds : angle 7.11864 ( 192) SS BOND : bond 0.00538 ( 3) SS BOND : angle 2.37097 ( 6) covalent geometry : bond 0.00399 ( 2415) covalent geometry : angle 0.60128 ( 3292) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.367 Fit side-chains REVERT: A 54 ARG cc_start: 0.9166 (mtt180) cc_final: 0.6763 (mmt90) REVERT: A 115 LYS cc_start: 0.8917 (mtmm) cc_final: 0.8705 (mttp) REVERT: A 178 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8395 (tppt) REVERT: A 187 LYS cc_start: 0.8746 (mtpt) cc_final: 0.8415 (mptp) REVERT: A 206 ARG cc_start: 0.9095 (mtm-85) cc_final: 0.7633 (mtp180) outliers start: 4 outliers final: 2 residues processed: 22 average time/residue: 3.6378 time to fit residues: 81.5988 Evaluate side-chains 22 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.1980 chunk 18 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.080487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.065155 restraints weight = 9490.041| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.03 r_work: 0.2765 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2430 Z= 0.120 Angle : 0.577 6.302 3334 Z= 0.298 Chirality : 0.044 0.209 401 Planarity : 0.003 0.028 392 Dihedral : 7.190 54.681 547 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.21 % Allowed : 7.29 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.22 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.34 (0.49), residues: 100 loop : -0.42 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 174 HIS 0.003 0.001 HIS A 201 PHE 0.012 0.001 PHE A 74 TYR 0.009 0.001 TYR A 203 ARG 0.001 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 7) link_NAG-ASN : angle 1.46415 ( 21) link_ALPHA1-6 : bond 0.00981 ( 1) link_ALPHA1-6 : angle 1.86292 ( 3) link_BETA1-4 : bond 0.00205 ( 3) link_BETA1-4 : angle 1.42975 ( 9) link_ALPHA1-3 : bond 0.00854 ( 1) link_ALPHA1-3 : angle 1.48607 ( 3) hydrogen bonds : bond 0.03697 ( 73) hydrogen bonds : angle 6.96574 ( 192) SS BOND : bond 0.00376 ( 3) SS BOND : angle 1.91817 ( 6) covalent geometry : bond 0.00259 ( 2415) covalent geometry : angle 0.55361 ( 3292) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.351 Fit side-chains REVERT: A 54 ARG cc_start: 0.9114 (mtt180) cc_final: 0.6746 (mmt90) REVERT: A 115 LYS cc_start: 0.8891 (mtmm) cc_final: 0.8679 (mttp) REVERT: A 187 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8416 (mptp) REVERT: A 206 ARG cc_start: 0.9070 (mtm-85) cc_final: 0.7632 (mtp180) outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 3.5406 time to fit residues: 82.9490 Evaluate side-chains 22 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 0 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 0.0770 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.080145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.064710 restraints weight = 9392.043| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.04 r_work: 0.2758 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9165 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2430 Z= 0.135 Angle : 0.580 6.381 3334 Z= 0.299 Chirality : 0.044 0.203 401 Planarity : 0.003 0.028 392 Dihedral : 7.073 55.623 547 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.21 % Allowed : 7.29 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.19 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.35 (0.49), residues: 100 loop : -0.39 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 174 HIS 0.003 0.001 HIS A 201 PHE 0.012 0.001 PHE A 121 TYR 0.009 0.001 TYR A 203 ARG 0.001 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 7) link_NAG-ASN : angle 1.51993 ( 21) link_ALPHA1-6 : bond 0.00981 ( 1) link_ALPHA1-6 : angle 1.81527 ( 3) link_BETA1-4 : bond 0.00212 ( 3) link_BETA1-4 : angle 1.49767 ( 9) link_ALPHA1-3 : bond 0.00818 ( 1) link_ALPHA1-3 : angle 1.54701 ( 3) hydrogen bonds : bond 0.03780 ( 73) hydrogen bonds : angle 6.95739 ( 192) SS BOND : bond 0.00417 ( 3) SS BOND : angle 1.88260 ( 6) covalent geometry : bond 0.00294 ( 2415) covalent geometry : angle 0.55483 ( 3292) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.369 Fit side-chains REVERT: A 54 ARG cc_start: 0.9133 (mtt180) cc_final: 0.6763 (mmt90) REVERT: A 115 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8688 (mttp) REVERT: A 187 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8404 (mptp) REVERT: A 206 ARG cc_start: 0.9071 (mtm-85) cc_final: 0.7655 (mtp180) outliers start: 3 outliers final: 2 residues processed: 21 average time/residue: 3.6440 time to fit residues: 78.6961 Evaluate side-chains 21 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 11 optimal weight: 0.4980 chunk 20 optimal weight: 0.1980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.080470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.065163 restraints weight = 9720.733| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.05 r_work: 0.2774 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2430 Z= 0.118 Angle : 0.563 5.925 3334 Z= 0.290 Chirality : 0.044 0.196 401 Planarity : 0.003 0.028 392 Dihedral : 6.857 54.512 547 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.81 % Allowed : 8.10 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.31 (0.48), residues: 100 loop : -0.43 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 174 HIS 0.003 0.001 HIS A 201 PHE 0.012 0.001 PHE A 121 TYR 0.009 0.001 TYR A 203 ARG 0.001 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 7) link_NAG-ASN : angle 1.44114 ( 21) link_ALPHA1-6 : bond 0.00990 ( 1) link_ALPHA1-6 : angle 1.81386 ( 3) link_BETA1-4 : bond 0.00198 ( 3) link_BETA1-4 : angle 1.44781 ( 9) link_ALPHA1-3 : bond 0.00822 ( 1) link_ALPHA1-3 : angle 1.44680 ( 3) hydrogen bonds : bond 0.03607 ( 73) hydrogen bonds : angle 6.89759 ( 192) SS BOND : bond 0.00360 ( 3) SS BOND : angle 1.76609 ( 6) covalent geometry : bond 0.00255 ( 2415) covalent geometry : angle 0.53975 ( 3292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6116.87 seconds wall clock time: 106 minutes 23.57 seconds (6383.57 seconds total)