Starting phenix.real_space_refine on Wed Jul 23 21:30:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8de9_27388/07_2025/8de9_27388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de9_27388/07_2025/8de9_27388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8de9_27388/07_2025/8de9_27388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de9_27388/07_2025/8de9_27388.map" model { file = "/net/cci-nas-00/data/ceres_data/8de9_27388/07_2025/8de9_27388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de9_27388/07_2025/8de9_27388.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 1 5.49 5 S 16 5.16 5 C 2760 2.51 5 N 626 2.21 5 O 709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 4115 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2035 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 7, 'TRANS': 251} Chain: "B" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2028 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {' K': 3, 'PEV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.34, per 1000 atoms: 0.81 Number of scatterers: 4115 At special positions: 0 Unit cell: (80.514, 97.128, 79.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 16 16.00 P 1 15.00 O 709 8.00 N 626 7.00 C 2760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS B 93 " 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 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 536.7 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 43 through 91 removed outlier: 3.569A pdb=" N ALA A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 95 through 113 Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 152 through 196 removed outlier: 3.561A pdb=" N ILE A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 202 through 234 removed outlier: 3.894A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 269 through 298 removed outlier: 3.702A pdb=" N ILE A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 91 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 95 through 113 removed outlier: 3.580A pdb=" N ALA B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 152 through 193 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 204 through 223 Processing helix chain 'B' and resid 223 through 235 removed outlier: 3.713A pdb=" N ALA B 227 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 Processing helix chain 'B' and resid 269 through 297 323 hydrogen bonds defined for protein. 969 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: 1.04 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 623 1.31 - 1.44: 1184 1.44 - 1.56: 2381 1.56 - 1.69: 3 1.69 - 1.81: 26 Bond restraints: 4217 Sorted by residual: bond pdb=" CA ILE B 264 " pdb=" C ILE B 264 " ideal model delta sigma weight residual 1.530 1.584 -0.053 1.12e-02 7.97e+03 2.27e+01 bond pdb=" C31 PEV A 401 " pdb=" O2 PEV A 401 " ideal model delta sigma weight residual 1.330 1.409 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C11 PEV A 401 " pdb=" O3 PEV A 401 " ideal model delta sigma weight residual 1.335 1.398 -0.063 2.00e-02 2.50e+03 9.77e+00 bond pdb=" CA THR A 251 " pdb=" C THR A 251 " ideal model delta sigma weight residual 1.525 1.488 0.037 1.40e-02 5.10e+03 7.01e+00 bond pdb=" N THR A 251 " pdb=" CA THR A 251 " ideal model delta sigma weight residual 1.461 1.431 0.031 1.49e-02 4.50e+03 4.26e+00 ... (remaining 4212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 5583 3.27 - 6.55: 121 6.55 - 9.82: 12 9.82 - 13.09: 4 13.09 - 16.36: 1 Bond angle restraints: 5721 Sorted by residual: angle pdb=" C ILE B 264 " pdb=" CA ILE B 264 " pdb=" CB ILE B 264 " ideal model delta sigma weight residual 112.19 102.19 10.00 1.15e+00 7.56e-01 7.56e+01 angle pdb=" N GLU B 263 " pdb=" CA GLU B 263 " pdb=" C GLU B 263 " ideal model delta sigma weight residual 111.17 122.10 -10.93 1.41e+00 5.03e-01 6.01e+01 angle pdb=" C GLU B 263 " pdb=" CA GLU B 263 " pdb=" CB GLU B 263 " ideal model delta sigma weight residual 112.06 101.34 10.72 1.57e+00 4.06e-01 4.66e+01 angle pdb=" N TRP A 199 " pdb=" CA TRP A 199 " pdb=" C TRP A 199 " ideal model delta sigma weight residual 108.52 118.91 -10.39 1.63e+00 3.76e-01 4.06e+01 angle pdb=" O3P PEV A 401 " pdb=" P PEV A 401 " pdb=" O4P PEV A 401 " ideal model delta sigma weight residual 93.57 109.93 -16.36 3.00e+00 1.11e-01 2.98e+01 ... (remaining 5716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.26: 2302 27.26 - 54.53: 105 54.53 - 81.79: 8 81.79 - 109.05: 0 109.05 - 136.32: 1 Dihedral angle restraints: 2416 sinusoidal: 947 harmonic: 1469 Sorted by residual: dihedral pdb=" CA GLN B 122 " pdb=" C GLN B 122 " pdb=" N GLU B 123 " pdb=" CA GLU B 123 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" C3 PEV A 401 " pdb=" C1 PEV A 401 " pdb=" C2 PEV A 401 " pdb=" O3P PEV A 401 " ideal model delta sinusoidal sigma weight residual 292.80 156.48 136.32 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" CA LEU B 68 " pdb=" C LEU B 68 " pdb=" N GLU B 69 " pdb=" CA GLU B 69 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 2413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 591 0.089 - 0.178: 68 0.178 - 0.266: 5 0.266 - 0.355: 1 0.355 - 0.444: 2 Chirality restraints: 667 Sorted by residual: chirality pdb=" CA THR A 251 " pdb=" N THR A 251 " pdb=" C THR A 251 " pdb=" CB THR A 251 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CA ILE B 264 " pdb=" N ILE B 264 " pdb=" C ILE B 264 " pdb=" CB ILE B 264 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA LEU A 249 " pdb=" N LEU A 249 " pdb=" C LEU A 249 " pdb=" CB LEU A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 664 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 119 " 0.057 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO A 120 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 120 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 120 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 115 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO A 116 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 196 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C PHE A 196 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE A 196 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL A 197 " -0.013 2.00e-02 2.50e+03 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.88: 1450 2.88 - 3.44: 5034 3.44 - 4.01: 7273 4.01 - 4.57: 10264 4.57 - 5.14: 14449 Nonbonded interactions: 38470 Sorted by model distance: nonbonded pdb=" OE2 GLU A 234 " pdb=" OH TYR A 266 " model vdw 2.309 3.040 nonbonded pdb=" O PRO A 116 " pdb=" NZ LYS B 84 " model vdw 2.335 3.120 nonbonded pdb=" NZ LYS A 84 " pdb=" O PRO B 116 " model vdw 2.349 3.120 nonbonded pdb=" C ILE A 264 " pdb=" OE1 GLU A 265 " model vdw 2.376 3.270 nonbonded pdb=" OE1 GLN A 231 " pdb=" OG SER A 241 " model vdw 2.414 3.040 ... (remaining 38465 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 297) selection = chain 'B' } 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 14.860 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.005 0.079 4218 Z= 0.268 Angle : 1.125 16.364 5723 Z= 0.634 Chirality : 0.059 0.444 667 Planarity : 0.008 0.088 685 Dihedral : 14.378 136.317 1475 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.23 % Allowed : 2.06 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.35), residues: 513 helix: 2.42 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -1.75 (0.51), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 127 HIS 0.006 0.001 HIS B 91 PHE 0.039 0.003 PHE A 276 TYR 0.016 0.002 TYR B 284 ARG 0.003 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.10107 ( 323) hydrogen bonds : angle 4.66508 ( 969) SS BOND : bond 0.00323 ( 1) SS BOND : angle 0.51756 ( 2) covalent geometry : bond 0.00537 ( 4217) covalent geometry : angle 1.12476 ( 5721) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8274 (tttt) cc_final: 0.7237 (ttmm) REVERT: A 77 LYS cc_start: 0.9185 (mttm) cc_final: 0.8964 (mtpt) REVERT: A 82 GLN cc_start: 0.8363 (pt0) cc_final: 0.7630 (pp30) REVERT: A 86 ASP cc_start: 0.8291 (m-30) cc_final: 0.7641 (m-30) REVERT: A 104 LYS cc_start: 0.9424 (ttpp) cc_final: 0.9104 (ttpp) REVERT: A 105 GLN cc_start: 0.8742 (mt0) cc_final: 0.8438 (pt0) REVERT: A 195 MET cc_start: 0.8544 (tmm) cc_final: 0.7513 (tmm) REVERT: A 268 ASP cc_start: 0.7318 (t70) cc_final: 0.6974 (t0) REVERT: B 66 LYS cc_start: 0.8656 (ttpt) cc_final: 0.8149 (ttmm) REVERT: B 120 PRO cc_start: 0.8391 (Cg_endo) cc_final: 0.7369 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1673 time to fit residues: 46.7294 Evaluate side-chains 193 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.0570 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.153433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.117010 restraints weight = 7231.876| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.80 r_work: 0.3367 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4218 Z= 0.177 Angle : 0.764 7.004 5723 Z= 0.401 Chirality : 0.045 0.197 667 Planarity : 0.005 0.042 685 Dihedral : 10.434 139.465 586 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.43 % Allowed : 16.02 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.36), residues: 513 helix: 2.69 (0.24), residues: 397 sheet: None (None), residues: 0 loop : -1.58 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 199 HIS 0.006 0.002 HIS B 91 PHE 0.022 0.002 PHE A 158 TYR 0.016 0.002 TYR B 266 ARG 0.002 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 323) hydrogen bonds : angle 4.05159 ( 969) SS BOND : bond 0.00215 ( 1) SS BOND : angle 0.31378 ( 2) covalent geometry : bond 0.00398 ( 4217) covalent geometry : angle 0.76443 ( 5721) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8410 (tttt) cc_final: 0.7473 (ttmm) REVERT: A 70 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8104 (mm110) REVERT: A 79 ARG cc_start: 0.8838 (tmt-80) cc_final: 0.8230 (tpt90) REVERT: A 82 GLN cc_start: 0.8731 (pt0) cc_final: 0.8049 (pp30) REVERT: A 83 GLU cc_start: 0.8488 (tp30) cc_final: 0.8240 (tp30) REVERT: A 86 ASP cc_start: 0.8495 (m-30) cc_final: 0.8161 (m-30) REVERT: A 95 GLN cc_start: 0.9037 (tp40) cc_final: 0.8124 (tp40) REVERT: A 101 ASP cc_start: 0.8892 (t0) cc_final: 0.8581 (t0) REVERT: A 104 LYS cc_start: 0.9471 (ttpp) cc_final: 0.9146 (ttpp) REVERT: A 153 GLU cc_start: 0.8166 (pm20) cc_final: 0.7900 (pm20) REVERT: A 180 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8165 (tp40) REVERT: A 221 LEU cc_start: 0.9410 (tt) cc_final: 0.9180 (pp) REVERT: A 240 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8335 (mt-10) REVERT: A 268 ASP cc_start: 0.8266 (t70) cc_final: 0.7955 (t70) REVERT: A 269 TYR cc_start: 0.8087 (m-80) cc_final: 0.7851 (m-80) REVERT: A 284 TYR cc_start: 0.8923 (t80) cc_final: 0.8564 (t80) REVERT: B 44 TRP cc_start: 0.7585 (m-90) cc_final: 0.7380 (m-10) REVERT: B 50 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8286 (tt) REVERT: B 66 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8186 (ttmt) REVERT: B 68 LEU cc_start: 0.9082 (mt) cc_final: 0.8864 (mp) REVERT: B 70 GLN cc_start: 0.9139 (mt0) cc_final: 0.8805 (mm-40) REVERT: B 115 ASN cc_start: 0.9256 (p0) cc_final: 0.9036 (p0) REVERT: B 122 GLN cc_start: 0.7337 (mp-120) cc_final: 0.6525 (mp10) REVERT: B 222 PHE cc_start: 0.8015 (m-80) cc_final: 0.7445 (m-10) REVERT: B 240 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8502 (mt-10) REVERT: B 284 TYR cc_start: 0.9159 (t80) cc_final: 0.8891 (t80) outliers start: 15 outliers final: 5 residues processed: 216 average time/residue: 0.1716 time to fit residues: 45.6266 Evaluate side-chains 205 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 198 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.0970 chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.153667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.116669 restraints weight = 7196.969| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.99 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4218 Z= 0.168 Angle : 0.779 11.096 5723 Z= 0.393 Chirality : 0.044 0.189 667 Planarity : 0.004 0.049 685 Dihedral : 10.339 135.827 586 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.66 % Allowed : 20.37 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.36), residues: 513 helix: 2.54 (0.24), residues: 399 sheet: None (None), residues: 0 loop : -1.29 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 295 HIS 0.001 0.001 HIS B 151 PHE 0.021 0.002 PHE A 158 TYR 0.021 0.002 TYR A 57 ARG 0.005 0.001 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 323) hydrogen bonds : angle 3.96294 ( 969) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.38513 ( 2) covalent geometry : bond 0.00382 ( 4217) covalent geometry : angle 0.77902 ( 5721) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8460 (tttt) cc_final: 0.7710 (ttmt) REVERT: A 70 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8074 (mm110) REVERT: A 82 GLN cc_start: 0.8621 (pt0) cc_final: 0.7796 (pp30) REVERT: A 86 ASP cc_start: 0.8496 (m-30) cc_final: 0.7897 (m-30) REVERT: A 101 ASP cc_start: 0.8807 (t0) cc_final: 0.8528 (t0) REVERT: A 104 LYS cc_start: 0.9466 (ttpp) cc_final: 0.9148 (ttpp) REVERT: A 284 TYR cc_start: 0.8746 (t80) cc_final: 0.8465 (t80) REVERT: B 43 LYS cc_start: 0.7992 (tptt) cc_final: 0.7069 (tptt) REVERT: B 45 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8190 (pttm) REVERT: B 48 LEU cc_start: 0.9101 (mt) cc_final: 0.8810 (mt) REVERT: B 66 LYS cc_start: 0.9080 (ttpt) cc_final: 0.8192 (ttmt) REVERT: B 70 GLN cc_start: 0.9017 (mt0) cc_final: 0.8705 (mm-40) REVERT: B 158 PHE cc_start: 0.9207 (t80) cc_final: 0.8964 (t80) REVERT: B 222 PHE cc_start: 0.8003 (m-80) cc_final: 0.7789 (m-10) REVERT: B 240 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8260 (mt-10) REVERT: B 295 TRP cc_start: 0.7846 (OUTLIER) cc_final: 0.7159 (m100) outliers start: 16 outliers final: 8 residues processed: 212 average time/residue: 0.1653 time to fit residues: 42.6684 Evaluate side-chains 203 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 295 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 95 GLN A 180 GLN A 232 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.143319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.109172 restraints weight = 7539.113| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 4.09 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4218 Z= 0.174 Angle : 0.808 9.992 5723 Z= 0.408 Chirality : 0.045 0.187 667 Planarity : 0.004 0.040 685 Dihedral : 10.266 132.236 586 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.89 % Allowed : 22.20 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.36), residues: 513 helix: 2.41 (0.24), residues: 399 sheet: None (None), residues: 0 loop : -1.36 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 295 HIS 0.007 0.001 HIS A 232 PHE 0.021 0.002 PHE A 158 TYR 0.019 0.002 TYR B 57 ARG 0.009 0.001 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 323) hydrogen bonds : angle 3.87217 ( 969) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.29969 ( 2) covalent geometry : bond 0.00407 ( 4217) covalent geometry : angle 0.80848 ( 5721) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8418 (tttt) cc_final: 0.7602 (ttmm) REVERT: A 70 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7978 (mm110) REVERT: A 75 LEU cc_start: 0.9191 (pp) cc_final: 0.8341 (pp) REVERT: A 79 ARG cc_start: 0.8534 (ttm110) cc_final: 0.8078 (ptp-110) REVERT: A 82 GLN cc_start: 0.8666 (pt0) cc_final: 0.7761 (pp30) REVERT: A 83 GLU cc_start: 0.8788 (tp30) cc_final: 0.8300 (tp30) REVERT: A 86 ASP cc_start: 0.8592 (m-30) cc_final: 0.7990 (m-30) REVERT: A 95 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: A 104 LYS cc_start: 0.9461 (ttpp) cc_final: 0.9213 (ttpp) REVERT: A 268 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.7684 (t70) REVERT: A 284 TYR cc_start: 0.8768 (t80) cc_final: 0.8509 (t80) REVERT: B 43 LYS cc_start: 0.7988 (tptt) cc_final: 0.7511 (tptt) REVERT: B 45 LYS cc_start: 0.8714 (mtmm) cc_final: 0.8357 (pttp) REVERT: B 48 LEU cc_start: 0.8970 (mt) cc_final: 0.8639 (mt) REVERT: B 66 LYS cc_start: 0.9013 (ttpt) cc_final: 0.8688 (ttpp) REVERT: B 70 GLN cc_start: 0.9115 (mt0) cc_final: 0.8751 (mm-40) REVERT: B 86 ASP cc_start: 0.9068 (p0) cc_final: 0.8797 (p0) REVERT: B 100 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8809 (mm-30) REVERT: B 104 LYS cc_start: 0.9391 (ttmm) cc_final: 0.9045 (mtmm) REVERT: B 158 PHE cc_start: 0.9205 (t80) cc_final: 0.8959 (t80) REVERT: B 222 PHE cc_start: 0.8014 (m-80) cc_final: 0.7782 (m-80) REVERT: B 240 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8263 (mt-10) REVERT: B 250 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.9043 (p) REVERT: B 291 MET cc_start: 0.8655 (tmm) cc_final: 0.7956 (mmp) outliers start: 17 outliers final: 7 residues processed: 214 average time/residue: 0.1613 time to fit residues: 42.0635 Evaluate side-chains 212 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 250 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 46 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.145833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110816 restraints weight = 7664.948| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 4.21 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4218 Z= 0.166 Angle : 0.831 9.873 5723 Z= 0.414 Chirality : 0.045 0.198 667 Planarity : 0.004 0.033 685 Dihedral : 10.139 129.991 586 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.75 % Allowed : 28.15 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.36), residues: 513 helix: 2.28 (0.24), residues: 399 sheet: None (None), residues: 0 loop : -1.47 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 295 HIS 0.002 0.001 HIS A 91 PHE 0.016 0.001 PHE B 196 TYR 0.022 0.002 TYR A 162 ARG 0.002 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 323) hydrogen bonds : angle 3.96011 ( 969) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.16412 ( 2) covalent geometry : bond 0.00376 ( 4217) covalent geometry : angle 0.83098 ( 5721) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7905 (mmtm) REVERT: A 66 LYS cc_start: 0.8448 (tttt) cc_final: 0.7593 (ttmm) REVERT: A 70 GLN cc_start: 0.8339 (mm110) cc_final: 0.8010 (mm110) REVERT: A 75 LEU cc_start: 0.9174 (pp) cc_final: 0.8390 (pp) REVERT: A 79 ARG cc_start: 0.8596 (ttm110) cc_final: 0.8163 (ptp-110) REVERT: A 82 GLN cc_start: 0.8639 (pt0) cc_final: 0.7829 (pp30) REVERT: A 83 GLU cc_start: 0.8728 (tp30) cc_final: 0.8314 (tp30) REVERT: A 86 ASP cc_start: 0.8599 (m-30) cc_final: 0.8144 (m-30) REVERT: A 104 LYS cc_start: 0.9447 (ttpp) cc_final: 0.9197 (ttpp) REVERT: A 174 LEU cc_start: 0.8551 (tp) cc_final: 0.8279 (tp) REVERT: A 179 ASP cc_start: 0.8621 (t0) cc_final: 0.8385 (t70) REVERT: A 268 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7251 (t70) REVERT: A 269 TYR cc_start: 0.7696 (m-80) cc_final: 0.7279 (m-80) REVERT: A 282 LEU cc_start: 0.8627 (mt) cc_final: 0.8417 (mt) REVERT: A 284 TYR cc_start: 0.8777 (t80) cc_final: 0.8513 (t80) REVERT: B 42 MET cc_start: 0.7932 (mmp) cc_final: 0.7724 (mmp) REVERT: B 43 LYS cc_start: 0.8109 (tptt) cc_final: 0.7480 (tptt) REVERT: B 45 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8266 (pttp) REVERT: B 48 LEU cc_start: 0.8956 (mt) cc_final: 0.8696 (mt) REVERT: B 58 LEU cc_start: 0.8584 (mt) cc_final: 0.8361 (mp) REVERT: B 66 LYS cc_start: 0.8976 (ttpt) cc_final: 0.8617 (ttpp) REVERT: B 70 GLN cc_start: 0.9172 (mt0) cc_final: 0.8854 (mm-40) REVERT: B 83 GLU cc_start: 0.8709 (pp20) cc_final: 0.8451 (pp20) REVERT: B 86 ASP cc_start: 0.8993 (p0) cc_final: 0.8642 (p0) REVERT: B 104 LYS cc_start: 0.9381 (ttmm) cc_final: 0.9047 (mtmm) REVERT: B 158 PHE cc_start: 0.9198 (t80) cc_final: 0.8962 (t80) REVERT: B 222 PHE cc_start: 0.8051 (m-80) cc_final: 0.7739 (m-10) REVERT: B 240 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8304 (mt-10) REVERT: B 250 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8979 (p) REVERT: B 291 MET cc_start: 0.8427 (tmm) cc_final: 0.7860 (mmp) outliers start: 12 outliers final: 7 residues processed: 211 average time/residue: 0.1694 time to fit residues: 43.3865 Evaluate side-chains 192 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 183 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 250 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 0.0170 chunk 43 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 35 optimal weight: 0.3980 chunk 33 optimal weight: 0.0370 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.148237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115079 restraints weight = 7528.981| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 4.01 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4218 Z= 0.159 Angle : 0.868 12.297 5723 Z= 0.416 Chirality : 0.046 0.229 667 Planarity : 0.004 0.035 685 Dihedral : 9.916 125.529 586 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.52 % Allowed : 30.89 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.36), residues: 513 helix: 2.17 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -1.56 (0.54), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 295 HIS 0.001 0.000 HIS A 91 PHE 0.019 0.001 PHE B 51 TYR 0.019 0.002 TYR A 162 ARG 0.002 0.000 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 323) hydrogen bonds : angle 3.96441 ( 969) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.16005 ( 2) covalent geometry : bond 0.00351 ( 4217) covalent geometry : angle 0.86839 ( 5721) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 TRP cc_start: 0.7297 (m-10) cc_final: 0.7077 (m-10) REVERT: A 45 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7898 (mmtm) REVERT: A 66 LYS cc_start: 0.8434 (tttt) cc_final: 0.7627 (ttmt) REVERT: A 70 GLN cc_start: 0.8350 (mm110) cc_final: 0.7866 (mm110) REVERT: A 75 LEU cc_start: 0.9194 (pp) cc_final: 0.8350 (pp) REVERT: A 79 ARG cc_start: 0.8546 (ttm110) cc_final: 0.8110 (ptp-110) REVERT: A 82 GLN cc_start: 0.8643 (pt0) cc_final: 0.7795 (pp30) REVERT: A 83 GLU cc_start: 0.8602 (tp30) cc_final: 0.8184 (tp30) REVERT: A 86 ASP cc_start: 0.8604 (m-30) cc_final: 0.8159 (m-30) REVERT: A 104 LYS cc_start: 0.9438 (ttpp) cc_final: 0.9185 (ttpp) REVERT: A 179 ASP cc_start: 0.8519 (t0) cc_final: 0.8289 (t0) REVERT: A 263 GLU cc_start: 0.8645 (tt0) cc_final: 0.8281 (tm-30) REVERT: A 268 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7540 (t70) REVERT: A 269 TYR cc_start: 0.7810 (m-80) cc_final: 0.7466 (m-80) REVERT: A 284 TYR cc_start: 0.8784 (t80) cc_final: 0.8547 (t80) REVERT: B 43 LYS cc_start: 0.7954 (tptt) cc_final: 0.7454 (tptt) REVERT: B 45 LYS cc_start: 0.8733 (mtmm) cc_final: 0.8287 (pttp) REVERT: B 48 LEU cc_start: 0.8951 (mt) cc_final: 0.8642 (mt) REVERT: B 66 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8139 (ttmt) REVERT: B 70 GLN cc_start: 0.9154 (mt0) cc_final: 0.8808 (mm-40) REVERT: B 86 ASP cc_start: 0.8934 (p0) cc_final: 0.8578 (p0) REVERT: B 104 LYS cc_start: 0.9344 (ttmm) cc_final: 0.9070 (mtmm) REVERT: B 180 GLN cc_start: 0.8836 (tt0) cc_final: 0.8397 (tp-100) REVERT: B 240 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8318 (mt-10) REVERT: B 250 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8930 (p) REVERT: B 282 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8156 (tp) outliers start: 11 outliers final: 6 residues processed: 199 average time/residue: 0.1754 time to fit residues: 42.3040 Evaluate side-chains 199 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.145532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.111995 restraints weight = 7639.741| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 4.08 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4218 Z= 0.179 Angle : 0.877 9.772 5723 Z= 0.432 Chirality : 0.045 0.175 667 Planarity : 0.004 0.034 685 Dihedral : 9.804 123.635 586 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.97 % Allowed : 30.89 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.36), residues: 513 helix: 2.14 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -1.54 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 199 HIS 0.002 0.000 HIS B 151 PHE 0.023 0.002 PHE B 51 TYR 0.021 0.002 TYR A 162 ARG 0.004 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 323) hydrogen bonds : angle 3.99179 ( 969) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.15298 ( 2) covalent geometry : bond 0.00419 ( 4217) covalent geometry : angle 0.87675 ( 5721) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7894 (mmtm) REVERT: A 66 LYS cc_start: 0.8456 (tttt) cc_final: 0.7603 (ttmm) REVERT: A 70 GLN cc_start: 0.8344 (mm110) cc_final: 0.7898 (mm110) REVERT: A 82 GLN cc_start: 0.8636 (pt0) cc_final: 0.7797 (pp30) REVERT: A 83 GLU cc_start: 0.8651 (tp30) cc_final: 0.8081 (tp30) REVERT: A 86 ASP cc_start: 0.8585 (m-30) cc_final: 0.8096 (m-30) REVERT: A 119 HIS cc_start: 0.8496 (t-90) cc_final: 0.8265 (t-90) REVERT: A 179 ASP cc_start: 0.8552 (t0) cc_final: 0.8317 (t0) REVERT: A 221 LEU cc_start: 0.9286 (tt) cc_final: 0.9061 (pp) REVERT: A 263 GLU cc_start: 0.8751 (tt0) cc_final: 0.8358 (tm-30) REVERT: A 268 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7622 (p0) REVERT: A 284 TYR cc_start: 0.8779 (t80) cc_final: 0.8497 (t80) REVERT: B 43 LYS cc_start: 0.8112 (tptt) cc_final: 0.7549 (tptt) REVERT: B 45 LYS cc_start: 0.8767 (mtmm) cc_final: 0.8324 (pttp) REVERT: B 48 LEU cc_start: 0.8997 (mt) cc_final: 0.8700 (mt) REVERT: B 66 LYS cc_start: 0.8966 (ttpt) cc_final: 0.8729 (ttpp) REVERT: B 70 GLN cc_start: 0.9172 (mt0) cc_final: 0.8824 (mm-40) REVERT: B 83 GLU cc_start: 0.8753 (pp20) cc_final: 0.8435 (pp20) REVERT: B 86 ASP cc_start: 0.9006 (p0) cc_final: 0.8648 (p0) REVERT: B 104 LYS cc_start: 0.9337 (ttmm) cc_final: 0.9061 (mtmm) REVERT: B 174 LEU cc_start: 0.9042 (tp) cc_final: 0.8717 (tp) REVERT: B 240 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8294 (mt-10) REVERT: B 250 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8975 (p) REVERT: B 291 MET cc_start: 0.8676 (tmm) cc_final: 0.7645 (mmp) outliers start: 13 outliers final: 7 residues processed: 193 average time/residue: 0.2024 time to fit residues: 47.6558 Evaluate side-chains 202 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 193 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 250 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 17 optimal weight: 0.0870 chunk 40 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.154333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.118726 restraints weight = 7226.557| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.81 r_work: 0.3412 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4218 Z= 0.172 Angle : 0.909 10.256 5723 Z= 0.452 Chirality : 0.046 0.193 667 Planarity : 0.004 0.036 685 Dihedral : 9.700 120.441 586 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.29 % Allowed : 30.89 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.36), residues: 513 helix: 2.12 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.65 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 295 HIS 0.001 0.000 HIS B 232 PHE 0.022 0.001 PHE B 222 TYR 0.022 0.002 TYR A 57 ARG 0.003 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 323) hydrogen bonds : angle 4.07176 ( 969) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.12531 ( 2) covalent geometry : bond 0.00383 ( 4217) covalent geometry : angle 0.90872 ( 5721) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7865 (mmtm) REVERT: A 66 LYS cc_start: 0.8752 (tttt) cc_final: 0.7946 (ttmm) REVERT: A 70 GLN cc_start: 0.8689 (mm110) cc_final: 0.8293 (mm110) REVERT: A 82 GLN cc_start: 0.8739 (pt0) cc_final: 0.7879 (pp30) REVERT: A 83 GLU cc_start: 0.8416 (tp30) cc_final: 0.8062 (tp30) REVERT: A 86 ASP cc_start: 0.8440 (m-30) cc_final: 0.8031 (m-30) REVERT: A 119 HIS cc_start: 0.8502 (t-90) cc_final: 0.8279 (t-90) REVERT: A 179 ASP cc_start: 0.8521 (t0) cc_final: 0.8296 (t0) REVERT: A 232 HIS cc_start: 0.7955 (t70) cc_final: 0.7738 (t70) REVERT: A 241 SER cc_start: 0.8848 (m) cc_final: 0.8272 (t) REVERT: A 263 GLU cc_start: 0.8714 (tt0) cc_final: 0.8255 (tm-30) REVERT: B 43 LYS cc_start: 0.8206 (tptt) cc_final: 0.7721 (tptt) REVERT: B 45 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8359 (pttp) REVERT: B 66 LYS cc_start: 0.9070 (ttpt) cc_final: 0.8234 (ttmt) REVERT: B 70 GLN cc_start: 0.9176 (mt0) cc_final: 0.8960 (mm-40) REVERT: B 104 LYS cc_start: 0.9330 (ttmm) cc_final: 0.9089 (mtmm) REVERT: B 180 GLN cc_start: 0.8929 (tt0) cc_final: 0.8592 (tp-100) REVERT: B 222 PHE cc_start: 0.8226 (m-10) cc_final: 0.7970 (m-10) REVERT: B 240 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8574 (mt-10) REVERT: B 291 MET cc_start: 0.8673 (tmm) cc_final: 0.7683 (mmp) outliers start: 10 outliers final: 7 residues processed: 207 average time/residue: 0.2935 time to fit residues: 74.2109 Evaluate side-chains 202 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 195 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.153031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.117831 restraints weight = 7438.962| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.79 r_work: 0.3391 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4218 Z= 0.185 Angle : 0.988 12.058 5723 Z= 0.485 Chirality : 0.049 0.292 667 Planarity : 0.004 0.035 685 Dihedral : 9.508 118.765 586 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.97 % Allowed : 32.27 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.36), residues: 513 helix: 1.94 (0.24), residues: 397 sheet: None (None), residues: 0 loop : -1.63 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 295 HIS 0.001 0.000 HIS B 151 PHE 0.024 0.002 PHE B 51 TYR 0.022 0.002 TYR B 57 ARG 0.006 0.001 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 323) hydrogen bonds : angle 4.19316 ( 969) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.26048 ( 2) covalent geometry : bond 0.00427 ( 4217) covalent geometry : angle 0.98861 ( 5721) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7825 (mmtm) REVERT: A 66 LYS cc_start: 0.8750 (tttt) cc_final: 0.8001 (ttmt) REVERT: A 70 GLN cc_start: 0.8746 (mm110) cc_final: 0.8312 (mm110) REVERT: A 82 GLN cc_start: 0.8740 (pt0) cc_final: 0.7803 (pp30) REVERT: A 83 GLU cc_start: 0.8563 (tp30) cc_final: 0.8160 (tp30) REVERT: A 86 ASP cc_start: 0.8441 (m-30) cc_final: 0.8014 (m-30) REVERT: A 119 HIS cc_start: 0.8502 (t-90) cc_final: 0.8280 (t-90) REVERT: A 179 ASP cc_start: 0.8574 (t0) cc_final: 0.8353 (t0) REVERT: A 232 HIS cc_start: 0.7939 (t70) cc_final: 0.7693 (t70) REVERT: A 263 GLU cc_start: 0.8711 (tt0) cc_final: 0.8476 (tm-30) REVERT: B 43 LYS cc_start: 0.8226 (tptt) cc_final: 0.7735 (tptt) REVERT: B 45 LYS cc_start: 0.8713 (mtmm) cc_final: 0.8303 (pttp) REVERT: B 48 LEU cc_start: 0.9063 (mt) cc_final: 0.8768 (mt) REVERT: B 66 LYS cc_start: 0.9072 (ttpt) cc_final: 0.8245 (ttmt) REVERT: B 70 GLN cc_start: 0.9196 (mt0) cc_final: 0.8938 (mm-40) REVERT: B 83 GLU cc_start: 0.8553 (pp20) cc_final: 0.8279 (pp20) REVERT: B 174 LEU cc_start: 0.9272 (tp) cc_final: 0.8894 (tp) REVERT: B 180 GLN cc_start: 0.8877 (tt0) cc_final: 0.8500 (tp-100) REVERT: B 222 PHE cc_start: 0.8266 (m-10) cc_final: 0.8042 (m-10) REVERT: B 240 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8576 (mt-10) REVERT: B 282 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8720 (tp) REVERT: B 291 MET cc_start: 0.8628 (tmm) cc_final: 0.7693 (mmp) outliers start: 13 outliers final: 8 residues processed: 194 average time/residue: 0.1921 time to fit residues: 44.6475 Evaluate side-chains 189 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.152979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.117220 restraints weight = 7328.879| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.83 r_work: 0.3393 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4218 Z= 0.187 Angle : 1.006 13.139 5723 Z= 0.494 Chirality : 0.048 0.307 667 Planarity : 0.004 0.031 685 Dihedral : 9.529 116.916 586 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.06 % Allowed : 33.87 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.36), residues: 513 helix: 1.88 (0.24), residues: 397 sheet: None (None), residues: 0 loop : -1.62 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 295 HIS 0.002 0.001 HIS B 119 PHE 0.021 0.001 PHE B 51 TYR 0.022 0.002 TYR B 57 ARG 0.005 0.001 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 323) hydrogen bonds : angle 4.25654 ( 969) SS BOND : bond 0.00088 ( 1) SS BOND : angle 0.24673 ( 2) covalent geometry : bond 0.00437 ( 4217) covalent geometry : angle 1.00576 ( 5721) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7844 (mmtm) REVERT: A 58 LEU cc_start: 0.9238 (mt) cc_final: 0.9014 (mt) REVERT: A 66 LYS cc_start: 0.8763 (tttt) cc_final: 0.7988 (ttmm) REVERT: A 70 GLN cc_start: 0.8746 (mm110) cc_final: 0.8304 (mm110) REVERT: A 82 GLN cc_start: 0.8770 (pt0) cc_final: 0.8309 (pp30) REVERT: A 119 HIS cc_start: 0.8383 (t-90) cc_final: 0.8180 (t-90) REVERT: A 179 ASP cc_start: 0.8549 (t0) cc_final: 0.8327 (t0) REVERT: A 207 ARG cc_start: 0.8777 (mpp80) cc_final: 0.8576 (mpp80) REVERT: A 263 GLU cc_start: 0.8761 (tt0) cc_final: 0.8439 (tm-30) REVERT: B 48 LEU cc_start: 0.9088 (mt) cc_final: 0.8804 (mt) REVERT: B 66 LYS cc_start: 0.9092 (ttpt) cc_final: 0.8271 (ttmt) REVERT: B 70 GLN cc_start: 0.9183 (mt0) cc_final: 0.8971 (mm-40) REVERT: B 180 GLN cc_start: 0.8925 (tt0) cc_final: 0.8557 (tp-100) REVERT: B 240 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8575 (mt-10) REVERT: B 282 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8701 (tp) REVERT: B 291 MET cc_start: 0.8627 (tmm) cc_final: 0.7907 (mmp) outliers start: 9 outliers final: 8 residues processed: 179 average time/residue: 0.2106 time to fit residues: 46.1959 Evaluate side-chains 185 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.152387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.116263 restraints weight = 7318.205| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.83 r_work: 0.3388 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4218 Z= 0.191 Angle : 0.998 12.938 5723 Z= 0.492 Chirality : 0.049 0.293 667 Planarity : 0.004 0.034 685 Dihedral : 9.539 114.973 586 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.06 % Allowed : 34.10 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.36), residues: 513 helix: 1.84 (0.24), residues: 397 sheet: None (None), residues: 0 loop : -1.74 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 295 HIS 0.002 0.001 HIS B 119 PHE 0.025 0.002 PHE A 158 TYR 0.022 0.002 TYR B 57 ARG 0.006 0.001 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 323) hydrogen bonds : angle 4.28783 ( 969) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.22859 ( 2) covalent geometry : bond 0.00448 ( 4217) covalent geometry : angle 0.99781 ( 5721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2733.40 seconds wall clock time: 49 minutes 42.24 seconds (2982.24 seconds total)