Starting phenix.real_space_refine on Wed Sep 17 03:19:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jtl_61811/09_2025/9jtl_61811.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jtl_61811/09_2025/9jtl_61811.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/9jtl_61811/09_2025/9jtl_61811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jtl_61811/09_2025/9jtl_61811.map" model { file = "/net/cci-nas-00/data/ceres_data/9jtl_61811/09_2025/9jtl_61811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jtl_61811/09_2025/9jtl_61811.cif" } resolution = 3.4 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 12 5.16 5 C 1870 2.51 5 N 443 2.21 5 O 477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2803 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2778 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P5S:plan-3': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.09, per 1000 atoms: 0.39 Number of scatterers: 2803 At special positions: 0 Unit cell: (69.7, 85.85, 66.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 1 15.00 O 477 8.00 N 443 7.00 C 1870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 245 " 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: 0.24 Conformation dependent library (CDL) restraints added in 115.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 650 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 71.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 5 through 23 removed outlier: 3.817A pdb=" N ASN A 22 " --> pdb=" O TYR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.989A pdb=" N HIS A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 77 removed outlier: 3.833A pdb=" N GLY A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 138 removed outlier: 4.174A pdb=" N VAL A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 173 Processing helix chain 'A' and resid 177 through 196 Processing helix chain 'A' and resid 205 through 229 Processing helix chain 'A' and resid 235 through 245 removed outlier: 4.431A pdb=" N GLU A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A 240 " --> pdb=" O TRP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 277 removed outlier: 3.915A pdb=" N LYS A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.827A pdb=" N ARG A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 310 removed outlier: 3.624A pdb=" N ARG A 295 " --> pdb=" O TRP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 336 Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.522A pdb=" N TYR A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) 173 hydrogen bonds defined for protein. 519 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: 0.35 Time building geometry restraints manager: 0.32 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: 414 1.31 - 1.44: 875 1.44 - 1.56: 1582 1.56 - 1.69: 2 1.69 - 1.82: 17 Bond restraints: 2890 Sorted by residual: bond pdb=" C17 P5S A 701 " pdb=" O19 P5S A 701 " ideal model delta sigma weight residual 1.351 1.416 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C17 P5S A 701 " pdb=" C20 P5S A 701 " ideal model delta sigma weight residual 1.505 1.549 -0.044 2.00e-02 2.50e+03 4.77e+00 bond pdb=" CG HIS A 176 " pdb=" CD2 HIS A 176 " ideal model delta sigma weight residual 1.354 1.331 0.023 1.10e-02 8.26e+03 4.50e+00 bond pdb=" N HIS A 176 " pdb=" CA HIS A 176 " ideal model delta sigma weight residual 1.455 1.480 -0.025 1.25e-02 6.40e+03 4.14e+00 bond pdb=" O15 P5S A 701 " pdb=" P12 P5S A 701 " ideal model delta sigma weight residual 1.493 1.452 0.041 2.00e-02 2.50e+03 4.12e+00 ... (remaining 2885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 3921 4.22 - 8.44: 14 8.44 - 12.67: 3 12.67 - 16.89: 0 16.89 - 21.11: 2 Bond angle restraints: 3940 Sorted by residual: angle pdb=" O13 P5S A 701 " pdb=" P12 P5S A 701 " pdb=" O15 P5S A 701 " ideal model delta sigma weight residual 121.25 100.14 21.11 3.00e+00 1.11e-01 4.95e+01 angle pdb=" O P5S A 701 " pdb=" C P5S A 701 " pdb=" OXT P5S A 701 " ideal model delta sigma weight residual 126.28 109.15 17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" CA HIS A 176 " pdb=" CB HIS A 176 " pdb=" CG HIS A 176 " ideal model delta sigma weight residual 113.80 118.04 -4.24 1.00e+00 1.00e+00 1.80e+01 angle pdb=" CA THR A 111 " pdb=" CB THR A 111 " pdb=" OG1 THR A 111 " ideal model delta sigma weight residual 109.60 103.64 5.96 1.50e+00 4.44e-01 1.58e+01 angle pdb=" OG P5S A 701 " pdb=" P12 P5S A 701 " pdb=" O16 P5S A 701 " ideal model delta sigma weight residual 102.49 112.08 -9.59 3.00e+00 1.11e-01 1.02e+01 ... (remaining 3935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.06: 1597 30.06 - 60.12: 48 60.12 - 90.17: 8 90.17 - 120.23: 1 120.23 - 150.29: 2 Dihedral angle restraints: 1656 sinusoidal: 647 harmonic: 1009 Sorted by residual: dihedral pdb=" CB P5S A 701 " pdb=" OG P5S A 701 " pdb=" P12 P5S A 701 " pdb=" O16 P5S A 701 " ideal model delta sinusoidal sigma weight residual -64.32 85.97 -150.29 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" CA TRP A 291 " pdb=" C TRP A 291 " pdb=" N LEU A 292 " pdb=" CA LEU A 292 " ideal model delta harmonic sigma weight residual -180.00 -158.21 -21.79 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C21 P5S A 701 " pdb=" C22 P5S A 701 " pdb=" C23 P5S A 701 " pdb=" C24 P5S A 701 " ideal model delta sinusoidal sigma weight residual -64.63 67.93 -132.56 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 1653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 299 0.036 - 0.072: 107 0.072 - 0.107: 29 0.107 - 0.143: 7 0.143 - 0.179: 1 Chirality restraints: 443 Sorted by residual: chirality pdb=" CA P5S A 701 " pdb=" N P5S A 701 " pdb=" C P5S A 701 " pdb=" CB P5S A 701 " both_signs ideal model delta sigma weight residual False 2.40 2.58 -0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA ASN A 203 " pdb=" N ASN A 203 " pdb=" C ASN A 203 " pdb=" CB ASN A 203 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.78e-01 chirality pdb=" CA ILE A 102 " pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CB ILE A 102 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 440 not shown) Planarity restraints: 476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 333 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO A 334 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 291 " 0.013 2.00e-02 2.50e+03 1.29e-02 4.19e+00 pdb=" CG TRP A 291 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 291 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 291 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 291 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 291 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 291 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 291 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 291 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 291 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 83 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO A 84 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 84 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 84 " 0.023 5.00e-02 4.00e+02 ... (remaining 473 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 622 2.78 - 3.31: 2657 3.31 - 3.84: 4410 3.84 - 4.37: 4718 4.37 - 4.90: 8740 Nonbonded interactions: 21147 Sorted by model distance: nonbonded pdb=" O LEU A 335 " pdb=" OG SER A 339 " model vdw 2.253 3.040 nonbonded pdb=" OD2 ASP A 254 " pdb=" OG1 THR A 256 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR A 280 " pdb=" NZ LYS A 285 " model vdw 2.439 3.120 nonbonded pdb=" OD1 ASP A 38 " pdb=" N LEU A 39 " model vdw 2.471 3.120 nonbonded pdb=" O ASP A 233 " pdb=" OD1 ASP A 233 " model vdw 2.515 3.040 ... (remaining 21142 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: 3.220 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.800 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 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 : 0.004 0.065 2891 Z= 0.216 Angle : 0.836 21.112 3942 Z= 0.395 Chirality : 0.041 0.179 443 Planarity : 0.005 0.055 476 Dihedral : 16.569 150.289 1003 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.33 % Allowed : 0.66 % Favored : 99.01 % 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 aren not related in a simple way. whole: 1.43 (0.49), residues: 342 helix: 2.55 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -2.51 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 243 TYR 0.009 0.001 TYR A 128 PHE 0.009 0.001 PHE A 309 TRP 0.035 0.002 TRP A 291 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 2890) covalent geometry : angle 0.83583 ( 3940) SS BOND : bond 0.00251 ( 1) SS BOND : angle 0.98224 ( 2) hydrogen bonds : bond 0.14645 ( 173) hydrogen bonds : angle 4.44333 ( 519) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.096 Fit side-chains REVERT: A 111 THR cc_start: 0.8453 (p) cc_final: 0.8190 (t) outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.0546 time to fit residues: 2.6629 Evaluate side-chains 34 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.0570 chunk 13 optimal weight: 0.0970 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.169427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.153062 restraints weight = 4022.484| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.72 r_work: 0.3568 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2891 Z= 0.125 Angle : 0.541 7.209 3942 Z= 0.281 Chirality : 0.039 0.123 443 Planarity : 0.004 0.037 476 Dihedral : 14.627 147.197 398 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.65 % Allowed : 7.26 % Favored : 91.09 % 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 aren not related in a simple way. whole: 1.73 (0.48), residues: 342 helix: 2.69 (0.35), residues: 231 sheet: None (None), residues: 0 loop : -2.46 (0.55), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 243 TYR 0.012 0.001 TYR A 224 PHE 0.008 0.001 PHE A 215 TRP 0.023 0.001 TRP A 291 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 2890) covalent geometry : angle 0.54073 ( 3940) SS BOND : bond 0.00206 ( 1) SS BOND : angle 0.73077 ( 2) hydrogen bonds : bond 0.05079 ( 173) hydrogen bonds : angle 3.51307 ( 519) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.100 Fit side-chains REVERT: A 22 ASN cc_start: 0.8031 (m-40) cc_final: 0.7638 (m-40) outliers start: 5 outliers final: 5 residues processed: 36 average time/residue: 0.0494 time to fit residues: 2.3208 Evaluate side-chains 37 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 290 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.170403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.154516 restraints weight = 4080.025| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.78 r_work: 0.3630 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2891 Z= 0.166 Angle : 0.570 7.583 3942 Z= 0.299 Chirality : 0.041 0.122 443 Planarity : 0.005 0.038 476 Dihedral : 13.769 152.709 398 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.31 % Allowed : 9.24 % Favored : 88.45 % 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 aren not related in a simple way. whole: 1.57 (0.48), residues: 342 helix: 2.62 (0.35), residues: 229 sheet: None (None), residues: 0 loop : -2.56 (0.54), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 243 TYR 0.012 0.002 TYR A 224 PHE 0.023 0.002 PHE A 223 TRP 0.019 0.001 TRP A 291 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 2890) covalent geometry : angle 0.56955 ( 3940) SS BOND : bond 0.00232 ( 1) SS BOND : angle 1.14917 ( 2) hydrogen bonds : bond 0.05653 ( 173) hydrogen bonds : angle 3.63767 ( 519) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.097 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 35 average time/residue: 0.0520 time to fit residues: 2.3331 Evaluate side-chains 37 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.0170 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.168801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.152827 restraints weight = 4036.484| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.69 r_work: 0.3549 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2891 Z= 0.125 Angle : 0.540 8.103 3942 Z= 0.279 Chirality : 0.040 0.123 443 Planarity : 0.004 0.041 476 Dihedral : 13.259 153.414 398 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.31 % Allowed : 10.23 % Favored : 87.46 % 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 aren not related in a simple way. whole: 1.68 (0.48), residues: 342 helix: 2.68 (0.34), residues: 230 sheet: None (None), residues: 0 loop : -2.50 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 243 TYR 0.008 0.001 TYR A 224 PHE 0.009 0.001 PHE A 223 TRP 0.016 0.001 TRP A 291 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 2890) covalent geometry : angle 0.54029 ( 3940) SS BOND : bond 0.00187 ( 1) SS BOND : angle 0.71989 ( 2) hydrogen bonds : bond 0.04899 ( 173) hydrogen bonds : angle 3.51829 ( 519) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.102 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 36 average time/residue: 0.0483 time to fit residues: 2.2907 Evaluate side-chains 37 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 9 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.167507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.151335 restraints weight = 4056.134| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.77 r_work: 0.3540 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2891 Z= 0.135 Angle : 0.567 12.673 3942 Z= 0.287 Chirality : 0.039 0.120 443 Planarity : 0.004 0.036 476 Dihedral : 12.916 155.506 398 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.64 % Allowed : 11.22 % Favored : 86.14 % 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 aren not related in a simple way. whole: 1.67 (0.48), residues: 342 helix: 2.64 (0.34), residues: 231 sheet: None (None), residues: 0 loop : -2.49 (0.54), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 243 TYR 0.010 0.001 TYR A 224 PHE 0.009 0.001 PHE A 223 TRP 0.015 0.001 TRP A 291 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 2890) covalent geometry : angle 0.56736 ( 3940) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.77738 ( 2) hydrogen bonds : bond 0.05017 ( 173) hydrogen bonds : angle 3.55828 ( 519) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.116 Fit side-chains REVERT: A 203 ASN cc_start: 0.7365 (p0) cc_final: 0.6982 (p0) outliers start: 8 outliers final: 6 residues processed: 34 average time/residue: 0.0570 time to fit residues: 2.5353 Evaluate side-chains 34 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.169376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.153502 restraints weight = 4016.883| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.72 r_work: 0.3555 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2891 Z= 0.121 Angle : 0.594 15.310 3942 Z= 0.286 Chirality : 0.039 0.119 443 Planarity : 0.004 0.033 476 Dihedral : 12.578 153.978 398 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.65 % Allowed : 13.20 % Favored : 85.15 % 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 aren not related in a simple way. whole: 1.75 (0.48), residues: 342 helix: 2.73 (0.34), residues: 231 sheet: None (None), residues: 0 loop : -2.52 (0.54), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 243 TYR 0.008 0.001 TYR A 93 PHE 0.007 0.001 PHE A 327 TRP 0.013 0.001 TRP A 291 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 2890) covalent geometry : angle 0.59370 ( 3940) SS BOND : bond 0.00189 ( 1) SS BOND : angle 0.59307 ( 2) hydrogen bonds : bond 0.04663 ( 173) hydrogen bonds : angle 3.48695 ( 519) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.096 Fit side-chains REVERT: A 203 ASN cc_start: 0.7256 (p0) cc_final: 0.6851 (p0) outliers start: 5 outliers final: 5 residues processed: 32 average time/residue: 0.0549 time to fit residues: 2.3075 Evaluate side-chains 34 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.165932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.150106 restraints weight = 4049.551| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.71 r_work: 0.3545 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 2891 Z= 0.147 Angle : 0.611 16.272 3942 Z= 0.302 Chirality : 0.040 0.121 443 Planarity : 0.004 0.035 476 Dihedral : 12.582 155.057 398 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.98 % Allowed : 13.20 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.48), residues: 342 helix: 2.65 (0.34), residues: 231 sheet: None (None), residues: 0 loop : -2.58 (0.54), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 243 TYR 0.011 0.001 TYR A 93 PHE 0.010 0.001 PHE A 215 TRP 0.014 0.001 TRP A 291 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 2890) covalent geometry : angle 0.61129 ( 3940) SS BOND : bond 0.00219 ( 1) SS BOND : angle 0.87909 ( 2) hydrogen bonds : bond 0.05197 ( 173) hydrogen bonds : angle 3.61113 ( 519) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.098 Fit side-chains REVERT: A 203 ASN cc_start: 0.7345 (p0) cc_final: 0.6935 (p0) outliers start: 6 outliers final: 6 residues processed: 34 average time/residue: 0.0517 time to fit residues: 2.2844 Evaluate side-chains 34 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.167199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.151310 restraints weight = 4101.626| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.72 r_work: 0.3538 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 2891 Z= 0.138 Angle : 0.631 16.731 3942 Z= 0.304 Chirality : 0.040 0.130 443 Planarity : 0.004 0.034 476 Dihedral : 12.452 154.601 398 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.98 % Allowed : 14.19 % Favored : 83.83 % 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 aren not related in a simple way. whole: 1.68 (0.48), residues: 342 helix: 2.69 (0.34), residues: 231 sheet: None (None), residues: 0 loop : -2.58 (0.54), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 243 TYR 0.009 0.001 TYR A 93 PHE 0.008 0.001 PHE A 215 TRP 0.013 0.001 TRP A 291 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 2890) covalent geometry : angle 0.63089 ( 3940) SS BOND : bond 0.00211 ( 1) SS BOND : angle 0.78679 ( 2) hydrogen bonds : bond 0.05018 ( 173) hydrogen bonds : angle 3.58839 ( 519) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.110 Fit side-chains REVERT: A 203 ASN cc_start: 0.7371 (p0) cc_final: 0.6973 (p0) outliers start: 6 outliers final: 6 residues processed: 35 average time/residue: 0.0527 time to fit residues: 2.3430 Evaluate side-chains 36 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 9 optimal weight: 0.0020 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.167759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.152383 restraints weight = 4111.745| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.65 r_work: 0.3561 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 2891 Z= 0.136 Angle : 0.638 14.544 3942 Z= 0.313 Chirality : 0.040 0.126 443 Planarity : 0.004 0.034 476 Dihedral : 12.309 153.450 398 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.31 % Allowed : 14.19 % Favored : 83.50 % 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 aren not related in a simple way. whole: 1.73 (0.48), residues: 342 helix: 2.74 (0.34), residues: 231 sheet: None (None), residues: 0 loop : -2.58 (0.53), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 243 TYR 0.009 0.001 TYR A 93 PHE 0.008 0.001 PHE A 223 TRP 0.013 0.001 TRP A 291 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 2890) covalent geometry : angle 0.63810 ( 3940) SS BOND : bond 0.00203 ( 1) SS BOND : angle 0.71196 ( 2) hydrogen bonds : bond 0.04896 ( 173) hydrogen bonds : angle 3.56580 ( 519) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.100 Fit side-chains REVERT: A 203 ASN cc_start: 0.7409 (p0) cc_final: 0.6984 (p0) outliers start: 7 outliers final: 7 residues processed: 37 average time/residue: 0.0536 time to fit residues: 2.5258 Evaluate side-chains 37 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 4 optimal weight: 0.0870 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.169254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.153456 restraints weight = 4070.975| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.69 r_work: 0.3584 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 2891 Z= 0.124 Angle : 0.610 14.071 3942 Z= 0.293 Chirality : 0.039 0.125 443 Planarity : 0.004 0.033 476 Dihedral : 12.009 151.954 398 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.31 % Allowed : 14.19 % Favored : 83.50 % 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 aren not related in a simple way. whole: 1.81 (0.48), residues: 342 helix: 2.78 (0.34), residues: 231 sheet: None (None), residues: 0 loop : -2.51 (0.54), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 243 TYR 0.008 0.001 TYR A 93 PHE 0.009 0.001 PHE A 223 TRP 0.013 0.001 TRP A 291 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 2890) covalent geometry : angle 0.61034 ( 3940) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.56513 ( 2) hydrogen bonds : bond 0.04556 ( 173) hydrogen bonds : angle 3.50090 ( 519) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.103 Fit side-chains REVERT: A 203 ASN cc_start: 0.7449 (p0) cc_final: 0.7015 (p0) REVERT: A 347 GLN cc_start: 0.5962 (mm-40) cc_final: 0.5056 (tm-30) outliers start: 7 outliers final: 7 residues processed: 37 average time/residue: 0.0541 time to fit residues: 2.5596 Evaluate side-chains 38 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 337 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 4 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.169631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.153877 restraints weight = 3982.988| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.70 r_work: 0.3580 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 2891 Z= 0.121 Angle : 0.609 14.311 3942 Z= 0.293 Chirality : 0.039 0.118 443 Planarity : 0.004 0.033 476 Dihedral : 11.549 150.669 398 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.31 % Allowed : 14.52 % Favored : 83.17 % 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 aren not related in a simple way. whole: 1.91 (0.48), residues: 342 helix: 2.86 (0.34), residues: 231 sheet: None (None), residues: 0 loop : -2.48 (0.54), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 243 TYR 0.007 0.001 TYR A 93 PHE 0.006 0.001 PHE A 327 TRP 0.013 0.001 TRP A 291 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 2890) covalent geometry : angle 0.60897 ( 3940) SS BOND : bond 0.00162 ( 1) SS BOND : angle 0.52421 ( 2) hydrogen bonds : bond 0.04413 ( 173) hydrogen bonds : angle 3.44502 ( 519) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 902.11 seconds wall clock time: 16 minutes 6.65 seconds (966.65 seconds total)