Starting phenix.real_space_refine on Wed Sep 17 03:19:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jtn_61813/09_2025/9jtn_61813.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jtn_61813/09_2025/9jtn_61813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jtn_61813/09_2025/9jtn_61813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jtn_61813/09_2025/9jtn_61813.map" model { file = "/net/cci-nas-00/data/ceres_data/9jtn_61813/09_2025/9jtn_61813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jtn_61813/09_2025/9jtn_61813.cif" } resolution = 3.1 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= -0.001 sd= 0.028 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 2 5.49 5 S 12 5.16 5 C 1876 2.51 5 N 441 2.21 5 O 482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 2813 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2769 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'PO4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Time building chain proxies: 0.89, per 1000 atoms: 0.32 Number of scatterers: 2813 At special positions: 0 Unit cell: (69.7, 77.35, 64.6, 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 2 15.00 O 482 8.00 N 441 7.00 C 1876 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: 0.31 Conformation dependent library (CDL) restraints added in 121.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 73.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 1 through 23 removed outlier: 3.736A pdb=" N MET A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.973A pdb=" N ALA A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.999A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 119 through 137 Processing helix chain 'A' and resid 148 through 173 removed outlier: 3.529A pdb=" N VAL A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 154 " --> pdb=" O CYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 196 Processing helix chain 'A' and resid 205 through 230 removed outlier: 3.571A pdb=" N TYR A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 258 through 276 removed outlier: 3.821A pdb=" N LEU A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 310 Processing helix chain 'A' and resid 318 through 339 removed outlier: 3.953A pdb=" N VAL A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 339 through 350 181 hydrogen bonds defined for protein. 537 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: 0.39 Time building geometry restraints manager: 0.36 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: 415 1.31 - 1.44: 875 1.44 - 1.56: 1590 1.56 - 1.69: 2 1.69 - 1.82: 17 Bond restraints: 2899 Sorted by residual: bond pdb=" O4 PO4 A 702 " pdb=" P PO4 A 702 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.68e+00 bond pdb=" O3 PO4 A 702 " pdb=" P PO4 A 702 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" O2 PO4 A 702 " pdb=" P PO4 A 702 " ideal model delta sigma weight residual 1.567 1.510 0.057 2.00e-02 2.50e+03 8.11e+00 bond pdb=" O1 PO4 A 702 " pdb=" P PO4 A 702 " ideal model delta sigma weight residual 1.565 1.510 0.055 2.00e-02 2.50e+03 7.65e+00 bond pdb=" C38 P5S A 701 " pdb=" O37 P5S A 701 " ideal model delta sigma weight residual 1.345 1.400 -0.055 2.00e-02 2.50e+03 7.44e+00 ... (remaining 2894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 3921 4.04 - 8.08: 27 8.08 - 12.12: 2 12.12 - 16.16: 0 16.16 - 20.20: 1 Bond angle restraints: 3951 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 121.25 101.05 20.20 3.00e+00 1.11e-01 4.53e+01 angle pdb=" CA TYR A 85 " pdb=" C TYR A 85 " pdb=" O TYR A 85 " ideal model delta sigma weight residual 119.97 116.24 3.73 1.15e+00 7.56e-01 1.05e+01 angle pdb=" C39 P5S A 701 " pdb=" C38 P5S A 701 " pdb=" O37 P5S A 701 " ideal model delta sigma weight residual 110.52 120.16 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C20 P5S A 701 " pdb=" C17 P5S A 701 " pdb=" O19 P5S A 701 " ideal model delta sigma weight residual 111.29 120.32 -9.03 3.00e+00 1.11e-01 9.06e+00 angle pdb=" C42 P5S A 701 " pdb=" C43 P5S A 701 " pdb=" C44 P5S A 701 " ideal model delta sigma weight residual 117.17 109.24 7.93 3.00e+00 1.11e-01 6.98e+00 ... (remaining 3946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.61: 1613 31.61 - 63.23: 38 63.23 - 94.84: 9 94.84 - 126.45: 3 126.45 - 158.06: 3 Dihedral angle restraints: 1666 sinusoidal: 660 harmonic: 1006 Sorted by residual: 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 93.43 -158.06 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C38 P5S A 701 " pdb=" C39 P5S A 701 " pdb=" C40 P5S A 701 " pdb=" C41 P5S A 701 " ideal model delta sinusoidal sigma weight residual 64.51 -84.19 148.70 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" C23 P5S A 701 " pdb=" C24 P5S A 701 " pdb=" C25 P5S A 701 " pdb=" C26 P5S A 701 " ideal model delta sinusoidal sigma weight residual -178.61 -48.25 -130.36 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 1663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 326 0.040 - 0.080: 91 0.080 - 0.120: 24 0.120 - 0.160: 1 0.160 - 0.200: 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 2.60 -0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA VAL A 99 " pdb=" N VAL A 99 " pdb=" C VAL A 99 " pdb=" CB VAL A 99 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.05e-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 3.55e-01 ... (remaining 440 not shown) Planarity restraints: 476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 292 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 293 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 293 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 293 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 86 " -0.011 2.00e-02 2.50e+03 8.93e-03 1.99e+00 pdb=" CG TRP A 86 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 86 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 86 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 84 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" C PRO A 84 " -0.022 2.00e-02 2.50e+03 pdb=" O PRO A 84 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR A 85 " 0.008 2.00e-02 2.50e+03 ... (remaining 473 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 342 2.75 - 3.29: 2641 3.29 - 3.83: 4525 3.83 - 4.36: 4941 4.36 - 4.90: 9088 Nonbonded interactions: 21537 Sorted by model distance: nonbonded pdb=" NZ LYS A 287 " pdb=" OG SER A 289 " model vdw 2.217 3.120 nonbonded pdb=" NZ LYS A 287 " pdb=" O SER A 289 " model vdw 2.338 3.120 nonbonded pdb=" OD1 ASP A 10 " pdb=" OH TYR A 94 " model vdw 2.344 3.040 nonbonded pdb=" OH TYR A 85 " pdb=" O GLU A 110 " model vdw 2.390 3.040 nonbonded pdb=" O SER A 316 " pdb=" OG SER A 316 " model vdw 2.433 3.040 ... (remaining 21532 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: 2.160 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.460 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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: 7.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 0.059 2900 Z= 0.204 Angle : 0.771 20.198 3953 Z= 0.329 Chirality : 0.040 0.200 443 Planarity : 0.004 0.054 476 Dihedral : 18.277 158.063 1015 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.08 (0.48), residues: 341 helix: 2.64 (0.36), residues: 237 sheet: None (None), residues: 0 loop : -1.81 (0.51), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.009 0.001 TYR A 85 PHE 0.007 0.001 PHE A 195 TRP 0.024 0.001 TRP A 86 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 2899) covalent geometry : angle 0.77070 ( 3951) SS BOND : bond 0.00255 ( 1) SS BOND : angle 0.81421 ( 2) hydrogen bonds : bond 0.16434 ( 181) hydrogen bonds : angle 5.15051 ( 537) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.103 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0413 time to fit residues: 1.8297 Evaluate side-chains 28 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.0060 chunk 30 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.155904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131768 restraints weight = 3406.430| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.91 r_work: 0.3356 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2900 Z= 0.110 Angle : 0.481 5.464 3953 Z= 0.243 Chirality : 0.039 0.121 443 Planarity : 0.004 0.054 476 Dihedral : 19.060 178.065 410 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.99 % Allowed : 5.96 % Favored : 93.05 % 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: 2.39 (0.47), residues: 341 helix: 2.72 (0.35), residues: 244 sheet: None (None), residues: 0 loop : -1.59 (0.54), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 281 TYR 0.006 0.001 TYR A 172 PHE 0.007 0.001 PHE A 148 TRP 0.025 0.001 TRP A 86 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 2899) covalent geometry : angle 0.48090 ( 3951) SS BOND : bond 0.00217 ( 1) SS BOND : angle 0.65230 ( 2) hydrogen bonds : bond 0.04876 ( 181) hydrogen bonds : angle 3.92631 ( 537) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.111 Fit side-chains REVERT: A 55 GLU cc_start: 0.7368 (mp0) cc_final: 0.7144 (mm-30) outliers start: 3 outliers final: 3 residues processed: 33 average time/residue: 0.0454 time to fit residues: 2.0251 Evaluate side-chains 31 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 150 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.0470 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.152614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.128142 restraints weight = 3440.846| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.92 r_work: 0.3287 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2900 Z= 0.129 Angle : 0.503 6.252 3953 Z= 0.251 Chirality : 0.040 0.123 443 Planarity : 0.004 0.050 476 Dihedral : 17.108 145.837 410 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.66 % Allowed : 7.62 % Favored : 90.73 % 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: 2.25 (0.47), residues: 341 helix: 2.64 (0.34), residues: 243 sheet: None (None), residues: 0 loop : -1.66 (0.53), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 281 TYR 0.006 0.001 TYR A 128 PHE 0.010 0.001 PHE A 159 TRP 0.024 0.001 TRP A 86 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 2899) covalent geometry : angle 0.50297 ( 3951) SS BOND : bond 0.00248 ( 1) SS BOND : angle 0.88553 ( 2) hydrogen bonds : bond 0.05539 ( 181) hydrogen bonds : angle 3.89776 ( 537) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.084 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 30 average time/residue: 0.0500 time to fit residues: 1.9499 Evaluate side-chains 32 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 249 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 29 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 0.0060 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 overall best weight: 0.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.157549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.133631 restraints weight = 3393.252| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.89 r_work: 0.3344 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2900 Z= 0.094 Angle : 0.438 5.181 3953 Z= 0.219 Chirality : 0.038 0.125 443 Planarity : 0.004 0.043 476 Dihedral : 16.270 150.766 410 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.99 % Allowed : 9.60 % Favored : 89.40 % 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: 2.63 (0.48), residues: 341 helix: 2.91 (0.34), residues: 243 sheet: None (None), residues: 0 loop : -1.48 (0.55), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 281 TYR 0.004 0.001 TYR A 18 PHE 0.005 0.001 PHE A 148 TRP 0.017 0.001 TRP A 86 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 2899) covalent geometry : angle 0.43773 ( 3951) SS BOND : bond 0.00188 ( 1) SS BOND : angle 0.63416 ( 2) hydrogen bonds : bond 0.04050 ( 181) hydrogen bonds : angle 3.74166 ( 537) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.125 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 33 average time/residue: 0.0493 time to fit residues: 2.1484 Evaluate side-chains 32 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 150 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.152601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128673 restraints weight = 3402.842| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.86 r_work: 0.3281 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2900 Z= 0.127 Angle : 0.496 5.899 3953 Z= 0.247 Chirality : 0.040 0.127 443 Planarity : 0.004 0.042 476 Dihedral : 16.341 153.899 410 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.32 % Allowed : 9.60 % Favored : 88.08 % 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: 2.38 (0.47), residues: 341 helix: 2.61 (0.34), residues: 249 sheet: None (None), residues: 0 loop : -1.49 (0.58), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 281 TYR 0.006 0.001 TYR A 128 PHE 0.010 0.001 PHE A 159 TRP 0.021 0.001 TRP A 86 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 2899) covalent geometry : angle 0.49552 ( 3951) SS BOND : bond 0.00316 ( 1) SS BOND : angle 0.94170 ( 2) hydrogen bonds : bond 0.05275 ( 181) hydrogen bonds : angle 3.81530 ( 537) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.155 Fit side-chains REVERT: A 135 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6450 (mt) outliers start: 7 outliers final: 5 residues processed: 33 average time/residue: 0.0534 time to fit residues: 2.3518 Evaluate side-chains 34 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 249 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.152702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128543 restraints weight = 3439.031| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.88 r_work: 0.3306 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2900 Z= 0.121 Angle : 0.485 5.938 3953 Z= 0.242 Chirality : 0.040 0.129 443 Planarity : 0.004 0.042 476 Dihedral : 16.399 156.738 410 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.32 % Allowed : 10.26 % Favored : 87.42 % 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: 2.50 (0.47), residues: 341 helix: 2.77 (0.34), residues: 243 sheet: None (None), residues: 0 loop : -1.42 (0.56), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.005 0.001 TYR A 128 PHE 0.008 0.001 PHE A 159 TRP 0.019 0.001 TRP A 86 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 2899) covalent geometry : angle 0.48448 ( 3951) SS BOND : bond 0.00313 ( 1) SS BOND : angle 0.91077 ( 2) hydrogen bonds : bond 0.05147 ( 181) hydrogen bonds : angle 3.80400 ( 537) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.080 Fit side-chains REVERT: A 135 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6402 (mt) outliers start: 7 outliers final: 5 residues processed: 34 average time/residue: 0.0496 time to fit residues: 2.2184 Evaluate side-chains 35 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 249 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.127534 restraints weight = 3362.896| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.87 r_work: 0.3295 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2900 Z= 0.142 Angle : 0.522 6.697 3953 Z= 0.260 Chirality : 0.041 0.135 443 Planarity : 0.004 0.043 476 Dihedral : 16.598 160.356 410 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.32 % Allowed : 10.26 % Favored : 87.42 % 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: 2.33 (0.47), residues: 341 helix: 2.66 (0.34), residues: 242 sheet: None (None), residues: 0 loop : -1.45 (0.55), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 281 TYR 0.007 0.001 TYR A 172 PHE 0.010 0.001 PHE A 159 TRP 0.020 0.001 TRP A 86 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 2899) covalent geometry : angle 0.52125 ( 3951) SS BOND : bond 0.00347 ( 1) SS BOND : angle 1.05971 ( 2) hydrogen bonds : bond 0.05804 ( 181) hydrogen bonds : angle 3.87705 ( 537) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.114 Fit side-chains REVERT: A 135 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6355 (mt) outliers start: 7 outliers final: 5 residues processed: 31 average time/residue: 0.0571 time to fit residues: 2.3302 Evaluate side-chains 32 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 249 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.0670 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 26 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 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.151149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126851 restraints weight = 3454.230| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.90 r_work: 0.3294 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2900 Z= 0.131 Angle : 0.505 6.340 3953 Z= 0.252 Chirality : 0.040 0.132 443 Planarity : 0.004 0.042 476 Dihedral : 16.564 162.490 410 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.32 % Allowed : 10.26 % Favored : 87.42 % 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: 2.36 (0.47), residues: 341 helix: 2.68 (0.34), residues: 242 sheet: None (None), residues: 0 loop : -1.43 (0.55), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.006 0.001 TYR A 172 PHE 0.009 0.001 PHE A 159 TRP 0.018 0.001 TRP A 86 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 2899) covalent geometry : angle 0.50432 ( 3951) SS BOND : bond 0.00322 ( 1) SS BOND : angle 0.95367 ( 2) hydrogen bonds : bond 0.05490 ( 181) hydrogen bonds : angle 3.86153 ( 537) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.107 Fit side-chains REVERT: A 135 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6353 (mt) outliers start: 7 outliers final: 6 residues processed: 31 average time/residue: 0.0519 time to fit residues: 2.1250 Evaluate side-chains 34 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 14 optimal weight: 0.0270 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 0.0270 chunk 9 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.154301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.130294 restraints weight = 3495.040| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.90 r_work: 0.3327 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2900 Z= 0.105 Angle : 0.458 5.279 3953 Z= 0.229 Chirality : 0.039 0.133 443 Planarity : 0.004 0.041 476 Dihedral : 16.412 168.303 410 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.32 % Allowed : 10.26 % Favored : 87.42 % 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: 2.44 (0.48), residues: 341 helix: 2.64 (0.34), residues: 249 sheet: None (None), residues: 0 loop : -1.44 (0.58), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.004 0.001 TYR A 172 PHE 0.006 0.001 PHE A 159 TRP 0.016 0.001 TRP A 86 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 2899) covalent geometry : angle 0.45735 ( 3951) SS BOND : bond 0.00245 ( 1) SS BOND : angle 0.72597 ( 2) hydrogen bonds : bond 0.04509 ( 181) hydrogen bonds : angle 3.76277 ( 537) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.112 Fit side-chains REVERT: A 135 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6309 (mt) outliers start: 7 outliers final: 5 residues processed: 33 average time/residue: 0.0553 time to fit residues: 2.4173 Evaluate side-chains 32 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 249 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.149427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.125210 restraints weight = 3501.192| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.89 r_work: 0.3281 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2900 Z= 0.153 Angle : 0.539 7.058 3953 Z= 0.270 Chirality : 0.041 0.136 443 Planarity : 0.004 0.042 476 Dihedral : 16.643 170.307 410 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.98 % Allowed : 9.60 % Favored : 87.42 % 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: 2.10 (0.47), residues: 341 helix: 2.38 (0.34), residues: 249 sheet: None (None), residues: 0 loop : -1.53 (0.57), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.007 0.001 TYR A 128 PHE 0.011 0.001 PHE A 159 TRP 0.020 0.001 TRP A 86 HIS 0.005 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 2899) covalent geometry : angle 0.53897 ( 3951) SS BOND : bond 0.00375 ( 1) SS BOND : angle 1.11020 ( 2) hydrogen bonds : bond 0.05991 ( 181) hydrogen bonds : angle 3.88820 ( 537) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 682 Ramachandran restraints generated. 341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.077 Fit side-chains REVERT: A 135 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6374 (mt) REVERT: A 281 ARG cc_start: 0.7959 (mtm110) cc_final: 0.7714 (mtm-85) outliers start: 9 outliers final: 8 residues processed: 32 average time/residue: 0.0363 time to fit residues: 1.5846 Evaluate side-chains 34 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125688 restraints weight = 3471.638| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.88 r_work: 0.3269 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2900 Z= 0.142 Angle : 0.523 6.655 3953 Z= 0.262 Chirality : 0.041 0.139 443 Planarity : 0.004 0.042 476 Dihedral : 16.633 171.111 410 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.98 % Allowed : 9.93 % Favored : 87.09 % 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: 2.10 (0.47), residues: 341 helix: 2.38 (0.34), residues: 249 sheet: None (None), residues: 0 loop : -1.52 (0.57), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.006 0.001 TYR A 128 PHE 0.010 0.001 PHE A 159 TRP 0.019 0.001 TRP A 86 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 2899) covalent geometry : angle 0.52296 ( 3951) SS BOND : bond 0.00342 ( 1) SS BOND : angle 1.02002 ( 2) hydrogen bonds : bond 0.05724 ( 181) hydrogen bonds : angle 3.89050 ( 537) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 845.45 seconds wall clock time: 15 minutes 12.79 seconds (912.79 seconds total)