Starting phenix.real_space_refine on Wed Sep 17 04:58:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bt2_44880/09_2025/9bt2_44880_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bt2_44880/09_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_44880/09_2025/9bt2_44880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bt2_44880/09_2025/9bt2_44880.map" model { file = "/net/cci-nas-00/data/ceres_data/9bt2_44880/09_2025/9bt2_44880_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bt2_44880/09_2025/9bt2_44880_trim.cif" } resolution = 1.93 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.94, per 1000 atoms: 0.21 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: 0.47 Conformation dependent library (CDL) restraints added in 101.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.14 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: 0.86 Time building geometry restraints manager: 0.58 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: 5.890 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: 0.030 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.060 Find NCS groups from input model: 0.010 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG A 206 TYR 0.113 0.019 TYR A 256 PHE 0.070 0.014 PHE A 74 TRP 0.115 0.021 TRP A 197 HIS 0.006 0.003 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.01468 ( 2415) covalent geometry : angle 1.64753 ( 3292) SS BOND : bond 0.01132 ( 3) SS BOND : angle 2.07968 ( 6) hydrogen bonds : bond 0.13609 ( 73) hydrogen bonds : angle 8.04005 ( 192) link_ALPHA1-3 : bond 0.02443 ( 1) link_ALPHA1-3 : angle 2.55948 ( 3) 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_NAG-ASN : bond 0.01043 ( 7) link_NAG-ASN : angle 4.33832 ( 21) *********************** 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 : 0.152 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: 1.7454 time to fit residues: 67.3232 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 : 0.128 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 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 = 0.3074 r_free = 0.3074 target = 0.077334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.061694 restraints weight = 9442.002| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.01 r_work: 0.2705 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9194 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 : 11.573 76.459 547 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 170 TYR 0.014 0.002 TYR A 50 PHE 0.019 0.002 PHE A 74 TRP 0.009 0.001 TRP A 174 HIS 0.004 0.002 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 2415) covalent geometry : angle 0.78446 ( 3292) SS BOND : bond 0.01255 ( 3) SS BOND : angle 5.21268 ( 6) hydrogen bonds : bond 0.05520 ( 73) hydrogen bonds : angle 7.68468 ( 192) link_ALPHA1-3 : bond 0.00983 ( 1) link_ALPHA1-3 : angle 2.26895 ( 3) link_ALPHA1-6 : bond 0.00717 ( 1) link_ALPHA1-6 : angle 1.83414 ( 3) link_BETA1-4 : bond 0.00182 ( 3) link_BETA1-4 : angle 2.38290 ( 9) link_NAG-ASN : bond 0.00436 ( 7) link_NAG-ASN : angle 2.17508 ( 21) *********************** 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 : 0.128 Fit side-chains REVERT: A 54 ARG cc_start: 0.9182 (mtt180) cc_final: 0.6815 (mmt90) REVERT: A 187 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8485 (mptp) REVERT: A 206 ARG cc_start: 0.9064 (mtm-85) cc_final: 0.7608 (mtp180) outliers start: 4 outliers final: 2 residues processed: 23 average time/residue: 1.9247 time to fit residues: 44.9575 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 : 0.131 ------------------------------------------------------------------------------- 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 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 12 optimal weight: 0.0270 chunk 11 optimal weight: 0.3980 overall best weight: 0.3638 ------------------------------------------------------------------------------- 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 = 0.3105 r_free = 0.3105 target = 0.078898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.063732 restraints weight = 9644.828| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.02 r_work: 0.2747 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 2430 Z= 0.148 Angle : 0.673 11.145 3334 Z= 0.349 Chirality : 0.046 0.253 401 Planarity : 0.003 0.031 392 Dihedral : 9.869 62.391 547 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.09 (0.51), residues: 97 loop : -0.28 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.011 0.001 TYR A 90 PHE 0.018 0.002 PHE A 74 TRP 0.006 0.001 TRP A 174 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 2415) covalent geometry : angle 0.64214 ( 3292) SS BOND : bond 0.00548 ( 3) SS BOND : angle 3.20597 ( 6) hydrogen bonds : bond 0.04396 ( 73) hydrogen bonds : angle 7.27547 ( 192) link_ALPHA1-3 : bond 0.01286 ( 1) link_ALPHA1-3 : angle 1.36096 ( 3) link_ALPHA1-6 : bond 0.00714 ( 1) link_ALPHA1-6 : angle 1.78401 ( 3) link_BETA1-4 : bond 0.00259 ( 3) link_BETA1-4 : angle 1.48190 ( 9) link_NAG-ASN : bond 0.00248 ( 7) link_NAG-ASN : angle 1.63099 ( 21) *********************** 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 : 0.132 Fit side-chains REVERT: A 26 ASN cc_start: 0.8428 (m-40) cc_final: 0.8166 (t0) REVERT: A 54 ARG cc_start: 0.9098 (mtt180) cc_final: 0.6680 (mmt90) REVERT: A 187 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8321 (mptp) REVERT: A 206 ARG cc_start: 0.9067 (mtm-85) cc_final: 0.7595 (mtp180) outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 1.7620 time to fit residues: 37.6524 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 : 0.124 ------------------------------------------------------------------------------- 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 5 optimal weight: 0.0470 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 9 optimal weight: 0.3980 overall best weight: 0.3278 ------------------------------------------------------------------------------- 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 = 0.3118 r_free = 0.3118 target = 0.079912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.064493 restraints weight = 9432.436| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.03 r_work: 0.2755 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 2430 Z= 0.145 Angle : 0.638 8.861 3334 Z= 0.326 Chirality : 0.046 0.226 401 Planarity : 0.003 0.029 392 Dihedral : 8.819 53.700 547 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.81 % Allowed : 7.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.13 (0.51), residues: 98 loop : -0.24 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 170 TYR 0.010 0.001 TYR A 38 PHE 0.016 0.001 PHE A 74 TRP 0.005 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 2415) covalent geometry : angle 0.60333 ( 3292) SS BOND : bond 0.00347 ( 3) SS BOND : angle 3.18701 ( 6) hydrogen bonds : bond 0.03976 ( 73) hydrogen bonds : angle 7.13079 ( 192) link_ALPHA1-3 : bond 0.00986 ( 1) link_ALPHA1-3 : angle 1.89523 ( 3) link_ALPHA1-6 : bond 0.00778 ( 1) link_ALPHA1-6 : angle 1.88693 ( 3) link_BETA1-4 : bond 0.00210 ( 3) link_BETA1-4 : angle 1.53988 ( 9) link_NAG-ASN : bond 0.00270 ( 7) link_NAG-ASN : angle 1.61743 ( 21) *********************** 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 20 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.086 Fit side-chains REVERT: A 54 ARG cc_start: 0.9105 (mtt180) cc_final: 0.6707 (mmt90) REVERT: A 187 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8330 (mptp) REVERT: A 206 ARG cc_start: 0.9066 (mtm-85) cc_final: 0.7550 (mtp180) outliers start: 2 outliers final: 2 residues processed: 20 average time/residue: 1.7311 time to fit residues: 35.1836 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 : 0.125 ------------------------------------------------------------------------------- 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 5 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3063 r_free = 0.3063 target = 0.076661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.061467 restraints weight = 9695.270| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.00 r_work: 0.2702 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 2430 Z= 0.215 Angle : 0.680 9.446 3334 Z= 0.347 Chirality : 0.046 0.219 401 Planarity : 0.004 0.029 392 Dihedral : 8.564 53.286 547 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.06 (0.50), residues: 98 loop : -0.26 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 54 TYR 0.014 0.002 TYR A 50 PHE 0.016 0.002 PHE A 74 TRP 0.005 0.001 TRP A 174 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 2415) covalent geometry : angle 0.64573 ( 3292) SS BOND : bond 0.00653 ( 3) SS BOND : angle 2.85876 ( 6) hydrogen bonds : bond 0.04631 ( 73) hydrogen bonds : angle 7.28513 ( 192) link_ALPHA1-3 : bond 0.00972 ( 1) link_ALPHA1-3 : angle 1.82777 ( 3) link_ALPHA1-6 : bond 0.00819 ( 1) link_ALPHA1-6 : angle 1.79035 ( 3) link_BETA1-4 : bond 0.00409 ( 3) link_BETA1-4 : angle 1.75066 ( 9) link_NAG-ASN : bond 0.00518 ( 7) link_NAG-ASN : angle 1.84155 ( 21) *********************** 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 23 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.155 Fit side-chains REVERT: A 54 ARG cc_start: 0.9186 (mtt180) cc_final: 0.6708 (mmt90) REVERT: A 187 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8338 (mptp) REVERT: A 206 ARG cc_start: 0.9099 (mtm-85) cc_final: 0.7572 (mtp180) outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 1.5496 time to fit residues: 34.7178 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 : 0.124 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.0670 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3076 r_free = 0.3076 target = 0.077371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.062231 restraints weight = 9868.615| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.02 r_work: 0.2723 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2430 Z= 0.166 Angle : 0.635 8.329 3334 Z= 0.327 Chirality : 0.045 0.220 401 Planarity : 0.003 0.028 392 Dihedral : 8.211 52.412 547 Min Nonbonded Distance : 2.469 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.05 (0.50), residues: 98 loop : -0.33 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 170 TYR 0.011 0.001 TYR A 50 PHE 0.014 0.001 PHE A 74 TRP 0.005 0.001 TRP A 174 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 2415) covalent geometry : angle 0.60522 ( 3292) SS BOND : bond 0.00535 ( 3) SS BOND : angle 2.54252 ( 6) hydrogen bonds : bond 0.04214 ( 73) hydrogen bonds : angle 7.17976 ( 192) link_ALPHA1-3 : bond 0.00939 ( 1) link_ALPHA1-3 : angle 1.67812 ( 3) link_ALPHA1-6 : bond 0.00855 ( 1) link_ALPHA1-6 : angle 1.84818 ( 3) link_BETA1-4 : bond 0.00252 ( 3) link_BETA1-4 : angle 1.54036 ( 9) link_NAG-ASN : bond 0.00332 ( 7) link_NAG-ASN : angle 1.66608 ( 21) *********************** 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 23 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.126 Fit side-chains REVERT: A 54 ARG cc_start: 0.9166 (mtt180) cc_final: 0.6708 (mmt90) REVERT: A 115 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8682 (mttp) REVERT: A 187 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8330 (mptp) REVERT: A 206 ARG cc_start: 0.9089 (mtm-85) cc_final: 0.7566 (mtp180) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 1.7575 time to fit residues: 39.3379 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 : 0.131 ------------------------------------------------------------------------------- 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 17 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 16 optimal weight: 0.0980 chunk 5 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 23 optimal weight: 0.4980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.3115 r_free = 0.3115 target = 0.079864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.064542 restraints weight = 9600.189| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.02 r_work: 0.2756 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9167 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2430 Z= 0.132 Angle : 0.591 6.798 3334 Z= 0.305 Chirality : 0.045 0.221 401 Planarity : 0.003 0.027 392 Dihedral : 7.578 52.819 547 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.03 (0.50), residues: 98 loop : -0.36 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 170 TYR 0.009 0.001 TYR A 203 PHE 0.014 0.001 PHE A 74 TRP 0.007 0.001 TRP A 174 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 2415) covalent geometry : angle 0.56577 ( 3292) SS BOND : bond 0.00405 ( 3) SS BOND : angle 2.06589 ( 6) hydrogen bonds : bond 0.03816 ( 73) hydrogen bonds : angle 7.05994 ( 192) link_ALPHA1-3 : bond 0.00939 ( 1) link_ALPHA1-3 : angle 1.58413 ( 3) link_ALPHA1-6 : bond 0.00953 ( 1) link_ALPHA1-6 : angle 1.88020 ( 3) link_BETA1-4 : bond 0.00201 ( 3) link_BETA1-4 : angle 1.46755 ( 9) link_NAG-ASN : bond 0.00241 ( 7) link_NAG-ASN : angle 1.52292 ( 21) *********************** 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 25 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.122 Fit side-chains REVERT: A 54 ARG cc_start: 0.9136 (mtt180) cc_final: 0.6768 (mmt90) REVERT: A 115 LYS cc_start: 0.8892 (mtmm) cc_final: 0.8676 (mttp) REVERT: A 187 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8397 (mptp) REVERT: A 206 ARG cc_start: 0.9084 (mtm-85) cc_final: 0.7641 (mtp180) outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 1.7502 time to fit residues: 42.6830 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 : 0.126 ------------------------------------------------------------------------------- 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 19 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 272 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.079097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.063699 restraints weight = 9645.717| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.03 r_work: 0.2740 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9179 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2430 Z= 0.159 Angle : 0.606 7.120 3334 Z= 0.311 Chirality : 0.045 0.214 401 Planarity : 0.004 0.028 392 Dihedral : 7.493 53.448 547 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.06 (0.50), residues: 98 loop : -0.34 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 34 TYR 0.010 0.001 TYR A 50 PHE 0.013 0.001 PHE A 74 TRP 0.006 0.001 TRP A 174 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 2415) covalent geometry : angle 0.57843 ( 3292) SS BOND : bond 0.00459 ( 3) SS BOND : angle 2.17829 ( 6) hydrogen bonds : bond 0.04006 ( 73) hydrogen bonds : angle 7.04310 ( 192) link_ALPHA1-3 : bond 0.00867 ( 1) link_ALPHA1-3 : angle 1.68317 ( 3) link_ALPHA1-6 : bond 0.00946 ( 1) link_ALPHA1-6 : angle 1.82540 ( 3) link_BETA1-4 : bond 0.00244 ( 3) link_BETA1-4 : angle 1.55244 ( 9) link_NAG-ASN : bond 0.00336 ( 7) link_NAG-ASN : angle 1.60482 ( 21) *********************** 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 23 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.123 Fit side-chains REVERT: A 54 ARG cc_start: 0.9156 (mtt180) cc_final: 0.6762 (mmt90) REVERT: A 115 LYS cc_start: 0.8909 (mtmm) cc_final: 0.8695 (mttp) REVERT: A 187 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8406 (mptp) REVERT: A 206 ARG cc_start: 0.9086 (mtm-85) cc_final: 0.7629 (mtp180) outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 1.9032 time to fit residues: 42.5186 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 : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 4 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3102 r_free = 0.3102 target = 0.079083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.063564 restraints weight = 9492.021| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.03 r_work: 0.2737 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9181 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2430 Z= 0.161 Angle : 0.607 7.161 3334 Z= 0.312 Chirality : 0.045 0.209 401 Planarity : 0.003 0.027 392 Dihedral : 7.375 53.913 547 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.05 (0.50), residues: 98 loop : -0.36 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.010 0.001 TYR A 50 PHE 0.013 0.001 PHE A 121 TRP 0.006 0.001 TRP A 174 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 2415) covalent geometry : angle 0.57992 ( 3292) SS BOND : bond 0.00475 ( 3) SS BOND : angle 2.17538 ( 6) hydrogen bonds : bond 0.04005 ( 73) hydrogen bonds : angle 7.07046 ( 192) link_ALPHA1-3 : bond 0.00837 ( 1) link_ALPHA1-3 : angle 1.58693 ( 3) link_ALPHA1-6 : bond 0.00951 ( 1) link_ALPHA1-6 : angle 1.80691 ( 3) link_BETA1-4 : bond 0.00256 ( 3) link_BETA1-4 : angle 1.56049 ( 9) link_NAG-ASN : bond 0.00334 ( 7) link_NAG-ASN : angle 1.60586 ( 21) *********************** 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 23 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.130 Fit side-chains REVERT: A 54 ARG cc_start: 0.9158 (mtt180) cc_final: 0.6764 (mmt90) REVERT: A 115 LYS cc_start: 0.8909 (mtmm) cc_final: 0.8695 (mttp) REVERT: A 187 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8420 (mptp) REVERT: A 206 ARG cc_start: 0.9086 (mtm-85) cc_final: 0.7661 (mtp180) outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 1.7004 time to fit residues: 38.0376 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 : 0.125 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 chunk 21 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 0 optimal weight: 0.0980 chunk 1 optimal weight: 0.0970 chunk 13 optimal weight: 0.5980 overall best weight: 0.1356 ------------------------------------------------------------------------------- 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 = 0.3156 r_free = 0.3156 target = 0.081933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.067108 restraints weight = 9790.218| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.02 r_work: 0.2811 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2430 Z= 0.100 Angle : 0.546 5.295 3334 Z= 0.281 Chirality : 0.044 0.201 401 Planarity : 0.003 0.029 392 Dihedral : 6.841 56.376 547 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.81 % Allowed : 7.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.13 (0.48), residues: 95 loop : -0.43 (0.50), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 34 TYR 0.008 0.001 TYR A 203 PHE 0.011 0.001 PHE A 74 TRP 0.007 0.001 TRP A 174 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 2415) covalent geometry : angle 0.52532 ( 3292) SS BOND : bond 0.00234 ( 3) SS BOND : angle 1.61079 ( 6) hydrogen bonds : bond 0.03364 ( 73) hydrogen bonds : angle 6.80807 ( 192) link_ALPHA1-3 : bond 0.00909 ( 1) link_ALPHA1-3 : angle 1.37928 ( 3) link_ALPHA1-6 : bond 0.00984 ( 1) link_ALPHA1-6 : angle 1.85877 ( 3) link_BETA1-4 : bond 0.00267 ( 3) link_BETA1-4 : angle 1.31938 ( 9) link_NAG-ASN : bond 0.00158 ( 7) link_NAG-ASN : angle 1.31599 ( 21) ********************** 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 23 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.123 Fit side-chains REVERT: A 54 ARG cc_start: 0.9100 (mtt180) cc_final: 0.6732 (mmt90) REVERT: A 115 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8648 (mtmm) REVERT: A 187 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8330 (mptp) REVERT: A 206 ARG cc_start: 0.9064 (mtm-85) cc_final: 0.7589 (mtp180) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 1.9499 time to fit residues: 43.5463 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 : 0.136 ------------------------------------------------------------------------------- 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 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 2 optimal weight: 0.4980 chunk 8 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3119 r_free = 0.3119 target = 0.079629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.064286 restraints weight = 9774.378| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.05 r_work: 0.2758 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.3365 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= 0.152 Angle : 0.582 6.280 3334 Z= 0.299 Chirality : 0.044 0.195 401 Planarity : 0.003 0.028 392 Dihedral : 6.945 56.733 547 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.62 % Allowed : 7.69 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.06 (0.48), residues: 98 loop : -0.35 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.010 0.001 TYR A 50 PHE 0.013 0.001 PHE A 121 TRP 0.005 0.001 TRP A 174 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 2415) covalent geometry : angle 0.55643 ( 3292) SS BOND : bond 0.00446 ( 3) SS BOND : angle 1.87145 ( 6) hydrogen bonds : bond 0.03833 ( 73) hydrogen bonds : angle 6.90467 ( 192) link_ALPHA1-3 : bond 0.00766 ( 1) link_ALPHA1-3 : angle 1.52119 ( 3) link_ALPHA1-6 : bond 0.01017 ( 1) link_ALPHA1-6 : angle 1.80865 ( 3) link_BETA1-4 : bond 0.00249 ( 3) link_BETA1-4 : angle 1.56403 ( 9) link_NAG-ASN : bond 0.00317 ( 7) link_NAG-ASN : angle 1.53800 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3044.56 seconds wall clock time: 52 minutes 17.44 seconds (3137.44 seconds total)