Starting phenix.real_space_refine on Tue Feb 3 13:21:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ws8_66194/02_2026/9ws8_66194.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ws8_66194/02_2026/9ws8_66194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ws8_66194/02_2026/9ws8_66194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ws8_66194/02_2026/9ws8_66194.map" model { file = "/net/cci-nas-00/data/ceres_data/9ws8_66194/02_2026/9ws8_66194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ws8_66194/02_2026/9ws8_66194.cif" } resolution = 3.47 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= -0.000 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2088 2.51 5 N 507 2.21 5 O 559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3175 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3175 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 16, 'TRANS': 399} Chain breaks: 1 Time building chain proxies: 0.84, per 1000 atoms: 0.26 Number of scatterers: 3175 At special positions: 0 Unit cell: (74.984, 58.504, 69.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 559 8.00 N 507 7.00 C 2088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.15 Conformation dependent library (CDL) restraints added in 83.0 milliseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 83.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 1 through 29 removed outlier: 3.627A pdb=" N TYR A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 29 " --> pdb=" O TYR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 34 through 42 removed outlier: 3.903A pdb=" N GLU A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 69 removed outlier: 3.750A pdb=" N LEU A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 77 through 96 Processing helix chain 'A' and resid 99 through 129 removed outlier: 4.071A pdb=" N TRP A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 133 through 160 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 164 through 187 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.595A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 247 removed outlier: 3.809A pdb=" N TRP A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 291 Processing helix chain 'A' and resid 300 through 321 Processing helix chain 'A' and resid 327 through 357 removed outlier: 3.533A pdb=" N ILE A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Proline residue: A 345 - end of helix Processing helix chain 'A' and resid 363 through 391 Proline residue: A 383 - end of helix Processing helix chain 'A' and resid 391 through 414 removed outlier: 3.937A pdb=" N THR A 395 " --> pdb=" O TYR A 391 " (cutoff:3.500A) 263 hydrogen bonds defined for protein. 783 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: 0.32 Time building geometry restraints manager: 0.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 936 1.34 - 1.46: 569 1.46 - 1.57: 1723 1.57 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 3263 Sorted by residual: bond pdb=" N VAL A 102 " pdb=" CA VAL A 102 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.15e+00 bond pdb=" N VAL A 100 " pdb=" CA VAL A 100 " ideal model delta sigma weight residual 1.464 1.499 -0.035 1.23e-02 6.61e+03 8.13e+00 bond pdb=" N SER A 97 " pdb=" CA SER A 97 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.21e-02 6.83e+03 7.61e+00 bond pdb=" N SER A 98 " pdb=" CA SER A 98 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.26e-02 6.30e+03 7.00e+00 bond pdb=" CA SER A 97 " pdb=" CB SER A 97 " ideal model delta sigma weight residual 1.531 1.491 0.040 1.52e-02 4.33e+03 6.79e+00 ... (remaining 3258 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 4151 1.57 - 3.14: 222 3.14 - 4.71: 44 4.71 - 6.28: 13 6.28 - 7.85: 9 Bond angle restraints: 4439 Sorted by residual: angle pdb=" N MET A 17 " pdb=" CA MET A 17 " pdb=" CB MET A 17 " ideal model delta sigma weight residual 110.28 117.87 -7.59 1.55e+00 4.16e-01 2.40e+01 angle pdb=" N PHE A 250 " pdb=" CA PHE A 250 " pdb=" C PHE A 250 " ideal model delta sigma weight residual 113.55 108.21 5.34 1.26e+00 6.30e-01 1.79e+01 angle pdb=" CA GLN A 248 " pdb=" C GLN A 248 " pdb=" N PHE A 249 " ideal model delta sigma weight residual 115.22 120.76 -5.54 1.43e+00 4.89e-01 1.50e+01 angle pdb=" CA MET A 17 " pdb=" CB MET A 17 " pdb=" CG MET A 17 " ideal model delta sigma weight residual 114.10 121.70 -7.60 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA GLN A 248 " pdb=" C GLN A 248 " pdb=" O GLN A 248 " ideal model delta sigma weight residual 122.03 117.80 4.23 1.13e+00 7.83e-01 1.40e+01 ... (remaining 4434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 1563 17.63 - 35.26: 225 35.26 - 52.90: 56 52.90 - 70.53: 8 70.53 - 88.16: 5 Dihedral angle restraints: 1857 sinusoidal: 677 harmonic: 1180 Sorted by residual: dihedral pdb=" CA LYS A 420 " pdb=" C LYS A 420 " pdb=" N MET A 421 " pdb=" CA MET A 421 " ideal model delta harmonic sigma weight residual -180.00 -156.44 -23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA GLY A 247 " pdb=" C GLY A 247 " pdb=" N GLN A 248 " pdb=" CA GLN A 248 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA TYR A 343 " pdb=" C TYR A 343 " pdb=" N GLY A 344 " pdb=" CA GLY A 344 " ideal model delta harmonic sigma weight residual 180.00 164.17 15.83 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 1854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 397 0.048 - 0.097: 87 0.097 - 0.145: 15 0.145 - 0.193: 1 0.193 - 0.241: 1 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA PRO A 201 " pdb=" N PRO A 201 " pdb=" C PRO A 201 " pdb=" CB PRO A 201 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB VAL A 100 " pdb=" CA VAL A 100 " pdb=" CG1 VAL A 100 " pdb=" CG2 VAL A 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CA MET A 17 " pdb=" N MET A 17 " pdb=" C MET A 17 " pdb=" CB MET A 17 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 498 not shown) Planarity restraints: 545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 344 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO A 345 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 200 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.11e+00 pdb=" N PRO A 201 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 201 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 201 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 107 " -0.016 2.00e-02 2.50e+03 1.67e-02 7.01e+00 pdb=" CG TRP A 107 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 107 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 107 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 107 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 107 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 107 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 107 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 107 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 107 " 0.000 2.00e-02 2.50e+03 ... (remaining 542 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 772 2.79 - 3.31: 3258 3.31 - 3.84: 5561 3.84 - 4.37: 6100 4.37 - 4.90: 10680 Nonbonded interactions: 26371 Sorted by model distance: nonbonded pdb=" O LEU A 317 " pdb=" OG1 THR A 321 " model vdw 2.258 3.040 nonbonded pdb=" NE1 TRP A 128 " pdb=" O HIS A 188 " model vdw 2.333 3.120 nonbonded pdb=" OG SER A 32 " pdb=" OD1 ASP A 245 " model vdw 2.352 3.040 nonbonded pdb=" OH TYR A 6 " pdb=" O ARG A 197 " model vdw 2.362 3.040 nonbonded pdb=" OG SER A 284 " pdb=" NE ARG A 300 " model vdw 2.374 3.120 ... (remaining 26366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.500 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 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 0.048 3263 Z= 0.264 Angle : 0.902 7.855 4439 Z= 0.570 Chirality : 0.042 0.241 501 Planarity : 0.007 0.083 545 Dihedral : 17.791 88.159 1107 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.58 % Favored : 94.17 % Rotamer: Outliers : 0.90 % Allowed : 24.48 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.98 (0.42), residues: 412 helix: 1.32 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -2.54 (0.66), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 319 TYR 0.018 0.002 TYR A 21 PHE 0.016 0.002 PHE A 33 TRP 0.042 0.002 TRP A 107 HIS 0.002 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 3263) covalent geometry : angle 0.90169 ( 4439) hydrogen bonds : bond 0.13654 ( 263) hydrogen bonds : angle 5.13634 ( 783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.105 Fit side-chains REVERT: A 391 TYR cc_start: 0.7012 (m-80) cc_final: 0.6811 (m-10) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.0663 time to fit residues: 2.8916 Evaluate side-chains 33 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 99 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.0570 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.4471 r_free = 0.4471 target = 0.215181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.192065 restraints weight = 2855.664| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 0.97 r_work: 0.4105 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3979 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3263 Z= 0.159 Angle : 0.662 7.838 4439 Z= 0.346 Chirality : 0.040 0.182 501 Planarity : 0.007 0.067 545 Dihedral : 4.991 39.990 444 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.10 % Favored : 94.66 % Rotamer: Outliers : 2.09 % Allowed : 23.88 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.34 (0.42), residues: 412 helix: 1.59 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -2.56 (0.69), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 166 TYR 0.019 0.001 TYR A 21 PHE 0.013 0.001 PHE A 33 TRP 0.013 0.001 TRP A 107 HIS 0.001 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 3263) covalent geometry : angle 0.66207 ( 4439) hydrogen bonds : bond 0.05112 ( 263) hydrogen bonds : angle 4.41974 ( 783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.164 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 38 average time/residue: 0.0650 time to fit residues: 3.0543 Evaluate side-chains 31 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.210845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.184966 restraints weight = 2868.346| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 1.11 r_work: 0.4042 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3921 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3263 Z= 0.177 Angle : 0.662 7.983 4439 Z= 0.344 Chirality : 0.041 0.177 501 Planarity : 0.006 0.064 545 Dihedral : 4.662 23.238 442 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.34 % Favored : 94.42 % Rotamer: Outliers : 4.48 % Allowed : 23.58 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.40 (0.42), residues: 412 helix: 1.61 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -2.50 (0.71), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 126 TYR 0.020 0.001 TYR A 21 PHE 0.012 0.001 PHE A 33 TRP 0.018 0.001 TRP A 107 HIS 0.002 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 3263) covalent geometry : angle 0.66239 ( 4439) hydrogen bonds : bond 0.04973 ( 263) hydrogen bonds : angle 4.33144 ( 783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.067 Fit side-chains REVERT: A 65 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.7212 (m-80) REVERT: A 125 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7155 (mp) outliers start: 15 outliers final: 5 residues processed: 46 average time/residue: 0.0590 time to fit residues: 3.2992 Evaluate side-chains 37 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 274 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 32 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4313 r_free = 0.4313 target = 0.205725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.180843 restraints weight = 2849.345| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 1.00 r_work: 0.3975 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3855 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3263 Z= 0.164 Angle : 0.645 8.094 4439 Z= 0.337 Chirality : 0.040 0.162 501 Planarity : 0.006 0.065 545 Dihedral : 4.633 22.533 442 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.37 % Favored : 95.39 % Rotamer: Outliers : 3.28 % Allowed : 24.78 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.43 (0.42), residues: 412 helix: 1.62 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -2.41 (0.71), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 10 TYR 0.016 0.001 TYR A 21 PHE 0.019 0.001 PHE A 33 TRP 0.016 0.001 TRP A 107 HIS 0.002 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3263) covalent geometry : angle 0.64486 ( 4439) hydrogen bonds : bond 0.04805 ( 263) hydrogen bonds : angle 4.31834 ( 783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.128 Fit side-chains REVERT: A 77 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6948 (mtp180) outliers start: 11 outliers final: 6 residues processed: 43 average time/residue: 0.1053 time to fit residues: 5.2839 Evaluate side-chains 39 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 274 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 19 optimal weight: 9.9990 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 = 0.4306 r_free = 0.4306 target = 0.205283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.181953 restraints weight = 2856.915| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 1.07 r_work: 0.3953 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3263 Z= 0.160 Angle : 0.647 8.253 4439 Z= 0.336 Chirality : 0.039 0.148 501 Planarity : 0.006 0.065 545 Dihedral : 4.573 21.935 442 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.85 % Favored : 94.90 % Rotamer: Outliers : 4.78 % Allowed : 23.28 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.49 (0.42), residues: 412 helix: 1.71 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -2.53 (0.69), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.016 0.001 TYR A 21 PHE 0.013 0.001 PHE A 14 TRP 0.021 0.001 TRP A 107 HIS 0.002 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3263) covalent geometry : angle 0.64695 ( 4439) hydrogen bonds : bond 0.04689 ( 263) hydrogen bonds : angle 4.23927 ( 783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 33 time to evaluate : 0.115 Fit side-chains REVERT: A 77 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7081 (mtp180) outliers start: 16 outliers final: 10 residues processed: 48 average time/residue: 0.0821 time to fit residues: 4.7452 Evaluate side-chains 42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 403 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.0670 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.207601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.185535 restraints weight = 2807.846| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 1.08 r_work: 0.4013 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3263 Z= 0.150 Angle : 0.633 8.916 4439 Z= 0.328 Chirality : 0.039 0.143 501 Planarity : 0.006 0.066 545 Dihedral : 4.577 21.519 442 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.61 % Favored : 95.15 % Rotamer: Outliers : 3.88 % Allowed : 25.07 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.67 (0.42), residues: 412 helix: 1.83 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -2.42 (0.69), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 10 TYR 0.015 0.001 TYR A 21 PHE 0.012 0.001 PHE A 14 TRP 0.021 0.001 TRP A 107 HIS 0.001 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3263) covalent geometry : angle 0.63276 ( 4439) hydrogen bonds : bond 0.04558 ( 263) hydrogen bonds : angle 4.21820 ( 783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.109 Fit side-chains REVERT: A 77 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.7058 (mtp180) outliers start: 13 outliers final: 9 residues processed: 46 average time/residue: 0.0856 time to fit residues: 4.7333 Evaluate side-chains 44 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 274 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.4453 r_free = 0.4453 target = 0.215584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.194707 restraints weight = 2867.113| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 0.86 r_work: 0.4090 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3956 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3263 Z= 0.142 Angle : 0.642 8.287 4439 Z= 0.330 Chirality : 0.039 0.138 501 Planarity : 0.006 0.066 545 Dihedral : 4.550 20.742 442 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.61 % Favored : 95.15 % Rotamer: Outliers : 3.28 % Allowed : 25.97 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.77 (0.42), residues: 412 helix: 1.84 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -2.18 (0.70), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 166 TYR 0.013 0.001 TYR A 21 PHE 0.012 0.001 PHE A 14 TRP 0.025 0.001 TRP A 107 HIS 0.001 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3263) covalent geometry : angle 0.64182 ( 4439) hydrogen bonds : bond 0.04434 ( 263) hydrogen bonds : angle 4.15281 ( 783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.111 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 43 average time/residue: 0.0568 time to fit residues: 3.0024 Evaluate side-chains 40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 274 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 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 = 0.4436 r_free = 0.4436 target = 0.214269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.191625 restraints weight = 2911.068| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 1.09 r_work: 0.4130 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4015 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3263 Z= 0.156 Angle : 0.646 8.403 4439 Z= 0.331 Chirality : 0.039 0.143 501 Planarity : 0.006 0.068 545 Dihedral : 4.569 20.504 442 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.18 % Allowed : 25.37 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.80 (0.42), residues: 412 helix: 1.88 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -2.13 (0.67), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.013 0.001 TYR A 21 PHE 0.012 0.001 PHE A 14 TRP 0.026 0.001 TRP A 107 HIS 0.002 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 3263) covalent geometry : angle 0.64646 ( 4439) hydrogen bonds : bond 0.04530 ( 263) hydrogen bonds : angle 4.18319 ( 783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.111 Fit side-chains REVERT: A 125 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.6977 (mt) outliers start: 14 outliers final: 6 residues processed: 46 average time/residue: 0.0756 time to fit residues: 4.2481 Evaluate side-chains 40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 274 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 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 = 0.4465 r_free = 0.4465 target = 0.214560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.188588 restraints weight = 2873.522| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 1.20 r_work: 0.4101 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3982 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3263 Z= 0.155 Angle : 0.644 8.773 4439 Z= 0.330 Chirality : 0.039 0.143 501 Planarity : 0.006 0.072 545 Dihedral : 4.578 20.041 442 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.39 % Allowed : 26.87 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.84 (0.42), residues: 412 helix: 1.90 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -2.05 (0.68), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 166 TYR 0.013 0.001 TYR A 21 PHE 0.011 0.001 PHE A 14 TRP 0.022 0.001 TRP A 107 HIS 0.001 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 3263) covalent geometry : angle 0.64403 ( 4439) hydrogen bonds : bond 0.04525 ( 263) hydrogen bonds : angle 4.19709 ( 783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.064 Fit side-chains REVERT: A 125 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.6902 (mt) REVERT: A 166 ARG cc_start: 0.8423 (mtt-85) cc_final: 0.8173 (mtp85) outliers start: 8 outliers final: 7 residues processed: 41 average time/residue: 0.0558 time to fit residues: 2.8497 Evaluate side-chains 41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 403 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 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 = 0.4446 r_free = 0.4446 target = 0.214994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.193913 restraints weight = 2845.948| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 0.92 r_work: 0.4167 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.4061 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3263 Z= 0.150 Angle : 0.638 8.468 4439 Z= 0.326 Chirality : 0.039 0.145 501 Planarity : 0.006 0.074 545 Dihedral : 4.566 19.430 442 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.09 % Allowed : 27.16 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.89 (0.42), residues: 412 helix: 1.92 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -1.97 (0.68), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 166 TYR 0.012 0.001 TYR A 21 PHE 0.011 0.001 PHE A 14 TRP 0.020 0.001 TRP A 107 HIS 0.001 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3263) covalent geometry : angle 0.63784 ( 4439) hydrogen bonds : bond 0.04455 ( 263) hydrogen bonds : angle 4.15206 ( 783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.112 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 40 average time/residue: 0.0698 time to fit residues: 3.4810 Evaluate side-chains 40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 403 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 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 = 0.4447 r_free = 0.4447 target = 0.215205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.192248 restraints weight = 2908.972| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 1.10 r_work: 0.4077 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3263 Z= 0.150 Angle : 0.636 8.522 4439 Z= 0.326 Chirality : 0.039 0.149 501 Planarity : 0.006 0.076 545 Dihedral : 4.543 18.825 442 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.39 % Allowed : 26.57 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.96 (0.42), residues: 412 helix: 1.92 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.83 (0.71), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.013 0.001 TYR A 21 PHE 0.011 0.001 PHE A 14 TRP 0.018 0.001 TRP A 107 HIS 0.001 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 3263) covalent geometry : angle 0.63628 ( 4439) hydrogen bonds : bond 0.04456 ( 263) hydrogen bonds : angle 4.13873 ( 783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 847.97 seconds wall clock time: 15 minutes 12.48 seconds (912.48 seconds total)