Starting phenix.real_space_refine on Thu Jul 2 00:00:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wx7_66332/07_2026/9wx7_66332.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wx7_66332/07_2026/9wx7_66332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wx7_66332/07_2026/9wx7_66332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wx7_66332/07_2026/9wx7_66332.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wx7_66332/07_2026/9wx7_66332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wx7_66332/07_2026/9wx7_66332.map" } resolution = 2.57 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= -0.003 sd= 0.132 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 2857 2.51 5 N 657 2.21 5 O 715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4265 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4263 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 26, 'TRANS': 513} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Chain breaks: 2 Time building chain proxies: 0.97, per 1000 atoms: 0.23 Number of scatterers: 4265 At special positions: 0 Unit cell: (85.36, 76.824, 68.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 1 11.00 O 715 8.00 N 657 7.00 C 2857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 166 " 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: 0.39 Conformation dependent library (CDL) restraints added in 162.8 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 982 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 79.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.537A pdb=" N LEU A 44 " --> pdb=" O TRP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 72 through 86 Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 86 through 102 removed outlier: 3.547A pdb=" N LEU A 90 " --> pdb=" O CYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.601A pdb=" N TRP A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 115 through 147 removed outlier: 3.993A pdb=" N GLY A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 4.190A pdb=" N HIS A 156 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 214 through 234 Processing helix chain 'A' and resid 247 through 264 removed outlier: 3.516A pdb=" N THR A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 removed outlier: 4.041A pdb=" N GLY A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 284 through 300 removed outlier: 4.242A pdb=" N TRP A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.824A pdb=" N TYR A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 353 Processing helix chain 'A' and resid 365 through 376 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 380 through 415 removed outlier: 3.563A pdb=" N TRP A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 439 Processing helix chain 'A' and resid 440 through 443 removed outlier: 3.790A pdb=" N THR A 443 " --> pdb=" O ILE A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.656A pdb=" N TRP A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 532 through 561 removed outlier: 3.839A pdb=" N SER A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 588 through 592 removed outlier: 3.513A pdb=" N TYR A 591 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 592 " --> pdb=" O GLY A 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 588 through 592' Processing sheet with id=AA1, first strand: chain 'A' and resid 525 through 526 290 hydrogen bonds defined for protein. 846 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: 0.45 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1244 1.34 - 1.46: 1003 1.46 - 1.58: 2095 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 4396 Sorted by residual: bond pdb=" N ILE A 325 " pdb=" CA ILE A 325 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.19e-02 7.06e+03 1.15e+01 bond pdb=" N GLN A 522 " pdb=" CA GLN A 522 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.05e-02 9.07e+03 1.12e+01 bond pdb=" CA SER A 298 " pdb=" CB SER A 298 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.55e-02 4.16e+03 8.07e+00 bond pdb=" N ASN A 134 " pdb=" CA ASN A 134 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.30e-02 5.92e+03 5.99e+00 bond pdb=" N ASN A 59 " pdb=" CA ASN A 59 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.33e-02 5.65e+03 5.76e+00 ... (remaining 4391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 5734 1.53 - 3.06: 194 3.06 - 4.58: 48 4.58 - 6.11: 15 6.11 - 7.64: 2 Bond angle restraints: 5993 Sorted by residual: angle pdb=" CA SER A 298 " pdb=" C SER A 298 " pdb=" O SER A 298 " ideal model delta sigma weight residual 120.82 116.64 4.18 1.05e+00 9.07e-01 1.59e+01 angle pdb=" C ILE A 131 " pdb=" N TYR A 132 " pdb=" CA TYR A 132 " ideal model delta sigma weight residual 122.06 115.73 6.33 1.86e+00 2.89e-01 1.16e+01 angle pdb=" CB LYS A 234 " pdb=" CG LYS A 234 " pdb=" CD LYS A 234 " ideal model delta sigma weight residual 111.30 118.94 -7.64 2.30e+00 1.89e-01 1.10e+01 angle pdb=" CA ASN A 134 " pdb=" CB ASN A 134 " pdb=" CG ASN A 134 " ideal model delta sigma weight residual 112.60 109.34 3.26 1.00e+00 1.00e+00 1.06e+01 angle pdb=" CA ILE A 325 " pdb=" C ILE A 325 " pdb=" O ILE A 325 " ideal model delta sigma weight residual 120.95 117.56 3.39 1.04e+00 9.25e-01 1.06e+01 ... (remaining 5988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.13: 2066 13.13 - 26.25: 260 26.25 - 39.38: 113 39.38 - 52.51: 42 52.51 - 65.64: 15 Dihedral angle restraints: 2496 sinusoidal: 946 harmonic: 1550 Sorted by residual: dihedral pdb=" C ASN A 134 " pdb=" N ASN A 134 " pdb=" CA ASN A 134 " pdb=" CB ASN A 134 " ideal model delta harmonic sigma weight residual -122.60 -131.01 8.41 0 2.50e+00 1.60e-01 1.13e+01 dihedral pdb=" CA TRP A 109 " pdb=" C TRP A 109 " pdb=" N LYS A 110 " pdb=" CA LYS A 110 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CG ARG A 587 " pdb=" CD ARG A 587 " pdb=" NE ARG A 587 " pdb=" CZ ARG A 587 " ideal model delta sinusoidal sigma weight residual 180.00 135.80 44.20 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 2493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 522 0.045 - 0.090: 108 0.090 - 0.134: 40 0.134 - 0.179: 3 0.179 - 0.224: 1 Chirality restraints: 674 Sorted by residual: chirality pdb=" CA ASN A 134 " pdb=" N ASN A 134 " pdb=" C ASN A 134 " pdb=" CB ASN A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE A 325 " pdb=" N ILE A 325 " pdb=" C ILE A 325 " pdb=" CB ILE A 325 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA VAL A 243 " pdb=" N VAL A 243 " pdb=" C VAL A 243 " pdb=" CB VAL A 243 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 671 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 522 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO A 523 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 523 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 523 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 471 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C LEU A 471 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU A 471 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 472 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 193 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.73e+00 pdb=" C TYR A 193 " 0.038 2.00e-02 2.50e+03 pdb=" O TYR A 193 " -0.014 2.00e-02 2.50e+03 pdb=" N TRP A 194 " -0.013 2.00e-02 2.50e+03 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 475 2.75 - 3.29: 4356 3.29 - 3.82: 7704 3.82 - 4.36: 9341 4.36 - 4.90: 15635 Nonbonded interactions: 37511 Sorted by model distance: nonbonded pdb=" OG SER A 147 " pdb=" OG SER A 385 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR A 79 " pdb="CL CL A 702 " model vdw 2.231 3.270 nonbonded pdb=" O ALA A 84 " pdb=" OH TYR A 497 " model vdw 2.254 3.040 nonbonded pdb=" OG SER A 298 " pdb="NA NA A 701 " model vdw 2.354 3.210 nonbonded pdb=" O LEU A 378 " pdb=" OG SER A 381 " model vdw 2.361 3.040 ... (remaining 37506 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: 1.660 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: 0.010 Set scattering table: 0.010 Process input model: 5.180 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: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 0.058 4397 Z= 0.240 Angle : 0.692 7.638 5995 Z= 0.423 Chirality : 0.043 0.224 674 Planarity : 0.006 0.065 726 Dihedral : 15.731 65.636 1511 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 20.53 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.36), residues: 536 helix: 1.21 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -1.45 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.016 0.001 TYR A 132 PHE 0.013 0.001 PHE A 245 TRP 0.027 0.002 TRP A 215 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.24 ( 4396) covalent geometry : angle 0.69180 / 0.42 ( 5993) SS BOND : bond 0.00149 / 0.08 ( 1) SS BOND : angle 0.47895 / 0.28 ( 2) hydrogen bonds : bond 0.11778 / 7.70 ( 290) hydrogen bonds : angle 5.58325 / 3.88 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.213 Fit side-chains REVERT: A 234 LYS cc_start: 0.7889 (tppt) cc_final: 0.6174 (tttm) REVERT: A 278 GLN cc_start: 0.8835 (mt0) cc_final: 0.8585 (mt0) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.4044 time to fit residues: 33.8207 Evaluate side-chains 67 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.0570 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS A 317 GLN A 373 GLN A 480 GLN A 522 GLN A 571 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106032 restraints weight = 4779.830| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.54 r_work: 0.3200 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4397 Z= 0.146 Angle : 0.530 5.818 5995 Z= 0.276 Chirality : 0.039 0.130 674 Planarity : 0.005 0.054 726 Dihedral : 4.217 21.396 584 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.31 % Allowed : 16.34 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.35), residues: 536 helix: 1.84 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -1.08 (0.46), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 568 TYR 0.015 0.002 TYR A 132 PHE 0.012 0.001 PHE A 245 TRP 0.016 0.002 TRP A 215 HIS 0.003 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 4396) covalent geometry : angle 0.53018 / 0.28 ( 5993) SS BOND : bond 0.00321 / 0.17 ( 1) SS BOND : angle 0.27680 / 0.16 ( 2) hydrogen bonds : bond 0.04834 / 3.15 ( 290) hydrogen bonds : angle 4.74834 / 3.28 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.112 Fit side-chains REVERT: A 94 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7159 (mt-10) REVERT: A 164 GLU cc_start: 0.8009 (pm20) cc_final: 0.7741 (pm20) REVERT: A 278 GLN cc_start: 0.8297 (mt0) cc_final: 0.8027 (mt0) REVERT: A 413 ASP cc_start: 0.8123 (m-30) cc_final: 0.7905 (m-30) REVERT: A 444 ASP cc_start: 0.8663 (m-30) cc_final: 0.8414 (m-30) outliers start: 15 outliers final: 4 residues processed: 74 average time/residue: 0.3710 time to fit residues: 28.7365 Evaluate side-chains 68 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 496 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 0.0030 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN A 400 GLN A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104299 restraints weight = 4747.597| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.52 r_work: 0.3184 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4397 Z= 0.144 Angle : 0.510 5.662 5995 Z= 0.263 Chirality : 0.038 0.132 674 Planarity : 0.005 0.049 726 Dihedral : 4.194 21.646 584 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.65 % Allowed : 16.56 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.35), residues: 536 helix: 2.01 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.88 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 568 TYR 0.016 0.002 TYR A 132 PHE 0.010 0.001 PHE A 229 TRP 0.018 0.002 TRP A 215 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 4396) covalent geometry : angle 0.50965 / 0.26 ( 5993) SS BOND : bond 0.00219 / 0.12 ( 1) SS BOND : angle 0.32106 / 0.19 ( 2) hydrogen bonds : bond 0.04789 / 3.11 ( 290) hydrogen bonds : angle 4.65440 / 3.22 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.165 Fit side-chains REVERT: A 164 GLU cc_start: 0.8042 (pm20) cc_final: 0.7786 (pm20) REVERT: A 413 ASP cc_start: 0.8161 (m-30) cc_final: 0.7927 (m-30) REVERT: A 444 ASP cc_start: 0.8822 (m-30) cc_final: 0.8541 (m-30) outliers start: 12 outliers final: 8 residues processed: 76 average time/residue: 0.3874 time to fit residues: 30.9425 Evaluate side-chains 73 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 525 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.117876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.103855 restraints weight = 4764.785| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.54 r_work: 0.3175 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4397 Z= 0.134 Angle : 0.493 5.608 5995 Z= 0.254 Chirality : 0.038 0.138 674 Planarity : 0.004 0.045 726 Dihedral : 4.146 20.734 584 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.53 % Allowed : 15.01 % Favored : 81.46 % 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 are not related in a simple way. whole: 1.89 (0.35), residues: 536 helix: 2.08 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.75 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 568 TYR 0.016 0.001 TYR A 132 PHE 0.008 0.001 PHE A 309 TRP 0.014 0.001 TRP A 215 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4396) covalent geometry : angle 0.49330 / 0.25 ( 5993) SS BOND : bond 0.00068 / 0.04 ( 1) SS BOND : angle 0.32675 / 0.19 ( 2) hydrogen bonds : bond 0.04596 / 2.98 ( 290) hydrogen bonds : angle 4.57489 / 3.18 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.106 Fit side-chains REVERT: A 116 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7583 (tttp) REVERT: A 164 GLU cc_start: 0.7937 (pm20) cc_final: 0.7668 (pm20) REVERT: A 234 LYS cc_start: 0.7205 (tppt) cc_final: 0.6334 (mmmt) REVERT: A 278 GLN cc_start: 0.8278 (mt0) cc_final: 0.7989 (mt0) REVERT: A 413 ASP cc_start: 0.8145 (m-30) cc_final: 0.7891 (m-30) REVERT: A 444 ASP cc_start: 0.8793 (m-30) cc_final: 0.8517 (m-30) outliers start: 16 outliers final: 9 residues processed: 77 average time/residue: 0.4225 time to fit residues: 33.9395 Evaluate side-chains 79 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 525 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112534 restraints weight = 4915.601| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.55 r_work: 0.3303 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4397 Z= 0.126 Angle : 0.481 5.568 5995 Z= 0.247 Chirality : 0.037 0.139 674 Planarity : 0.004 0.043 726 Dihedral : 4.092 20.163 584 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.09 % Allowed : 15.45 % Favored : 81.46 % 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 are not related in a simple way. whole: 1.98 (0.36), residues: 536 helix: 2.13 (0.25), residues: 375 sheet: None (None), residues: 0 loop : -0.67 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 568 TYR 0.016 0.001 TYR A 132 PHE 0.009 0.001 PHE A 309 TRP 0.015 0.001 TRP A 215 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 4396) covalent geometry : angle 0.48151 / 0.25 ( 5993) SS BOND : bond 0.00033 / 0.02 ( 1) SS BOND : angle 0.31261 / 0.17 ( 2) hydrogen bonds : bond 0.04470 / 2.89 ( 290) hydrogen bonds : angle 4.51206 / 3.14 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.102 Fit side-chains REVERT: A 116 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7699 (tttp) REVERT: A 164 GLU cc_start: 0.8056 (pm20) cc_final: 0.7796 (pm20) REVERT: A 167 LEU cc_start: 0.7964 (mt) cc_final: 0.7685 (mt) REVERT: A 234 LYS cc_start: 0.7169 (tppt) cc_final: 0.6379 (mmmt) REVERT: A 278 GLN cc_start: 0.8435 (mt0) cc_final: 0.8168 (mt0) REVERT: A 413 ASP cc_start: 0.8332 (m-30) cc_final: 0.8097 (m-30) REVERT: A 444 ASP cc_start: 0.8905 (m-30) cc_final: 0.8647 (m-30) outliers start: 14 outliers final: 10 residues processed: 78 average time/residue: 0.3984 time to fit residues: 32.4800 Evaluate side-chains 80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 525 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110799 restraints weight = 4982.004| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.57 r_work: 0.3286 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4397 Z= 0.151 Angle : 0.502 5.826 5995 Z= 0.258 Chirality : 0.038 0.144 674 Planarity : 0.004 0.043 726 Dihedral : 4.191 20.061 584 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.09 % Allowed : 15.45 % Favored : 81.46 % 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 are not related in a simple way. whole: 1.92 (0.35), residues: 536 helix: 2.07 (0.25), residues: 375 sheet: None (None), residues: 0 loop : -0.65 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 196 TYR 0.017 0.002 TYR A 132 PHE 0.011 0.001 PHE A 309 TRP 0.016 0.002 TRP A 215 HIS 0.002 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 4396) covalent geometry : angle 0.50191 / 0.26 ( 5993) SS BOND : bond 0.00030 / 0.02 ( 1) SS BOND : angle 0.33638 / 0.19 ( 2) hydrogen bonds : bond 0.04734 / 3.06 ( 290) hydrogen bonds : angle 4.61370 / 3.21 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.157 Fit side-chains REVERT: A 94 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: A 164 GLU cc_start: 0.8041 (pm20) cc_final: 0.7769 (pm20) REVERT: A 167 LEU cc_start: 0.8044 (mt) cc_final: 0.7806 (mt) REVERT: A 214 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7241 (mmp-170) REVERT: A 278 GLN cc_start: 0.8468 (mt0) cc_final: 0.8182 (mt0) REVERT: A 413 ASP cc_start: 0.8359 (m-30) cc_final: 0.8105 (m-30) REVERT: A 444 ASP cc_start: 0.8901 (m-30) cc_final: 0.8687 (m-30) outliers start: 14 outliers final: 9 residues processed: 74 average time/residue: 0.4791 time to fit residues: 36.9485 Evaluate side-chains 77 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 525 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 0.0270 chunk 24 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113152 restraints weight = 4951.636| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.57 r_work: 0.3315 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4397 Z= 0.117 Angle : 0.470 5.484 5995 Z= 0.241 Chirality : 0.037 0.140 674 Planarity : 0.004 0.043 726 Dihedral : 4.043 19.687 584 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.09 % Allowed : 15.89 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.36), residues: 536 helix: 2.18 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.57 (0.49), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.016 0.001 TYR A 132 PHE 0.012 0.001 PHE A 309 TRP 0.017 0.001 TRP A 215 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 4396) covalent geometry : angle 0.47030 / 0.24 ( 5993) SS BOND : bond 0.00011 / 0.01 ( 1) SS BOND : angle 0.20660 / 0.11 ( 2) hydrogen bonds : bond 0.04345 / 2.80 ( 290) hydrogen bonds : angle 4.45335 / 3.10 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.097 Fit side-chains REVERT: A 116 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7740 (tttp) REVERT: A 164 GLU cc_start: 0.8028 (pm20) cc_final: 0.7750 (pm20) REVERT: A 167 LEU cc_start: 0.8034 (mt) cc_final: 0.7795 (mt) REVERT: A 214 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7255 (mmp-170) REVERT: A 278 GLN cc_start: 0.8450 (mt0) cc_final: 0.8186 (mt0) REVERT: A 413 ASP cc_start: 0.8390 (m-30) cc_final: 0.8106 (m-30) REVERT: A 444 ASP cc_start: 0.8904 (m-30) cc_final: 0.8660 (m-30) outliers start: 14 outliers final: 10 residues processed: 78 average time/residue: 0.3693 time to fit residues: 30.1602 Evaluate side-chains 81 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 496 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 0.0870 chunk 12 optimal weight: 0.0970 chunk 45 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113332 restraints weight = 4926.102| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.56 r_work: 0.3313 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4397 Z= 0.118 Angle : 0.472 5.571 5995 Z= 0.242 Chirality : 0.037 0.139 674 Planarity : 0.004 0.043 726 Dihedral : 4.009 19.630 584 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.31 % Allowed : 15.89 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.36), residues: 536 helix: 2.23 (0.25), residues: 375 sheet: None (None), residues: 0 loop : -0.50 (0.49), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.016 0.001 TYR A 132 PHE 0.013 0.001 PHE A 309 TRP 0.019 0.001 TRP A 215 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 4396) covalent geometry : angle 0.47187 / 0.24 ( 5993) SS BOND : bond 0.00011 / 0.01 ( 1) SS BOND : angle 0.21142 / 0.11 ( 2) hydrogen bonds : bond 0.04331 / 2.80 ( 290) hydrogen bonds : angle 4.43998 / 3.09 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.130 Fit side-chains REVERT: A 164 GLU cc_start: 0.8047 (pm20) cc_final: 0.7765 (pm20) REVERT: A 212 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: A 214 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7237 (mmp-170) REVERT: A 278 GLN cc_start: 0.8426 (mt0) cc_final: 0.8154 (mt0) REVERT: A 413 ASP cc_start: 0.8353 (m-30) cc_final: 0.8085 (m-30) REVERT: A 444 ASP cc_start: 0.8878 (m-30) cc_final: 0.8636 (m-30) outliers start: 15 outliers final: 9 residues processed: 76 average time/residue: 0.3833 time to fit residues: 30.4740 Evaluate side-chains 80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 525 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.112869 restraints weight = 4976.452| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.57 r_work: 0.3310 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4397 Z= 0.124 Angle : 0.483 5.598 5995 Z= 0.247 Chirality : 0.037 0.140 674 Planarity : 0.004 0.043 726 Dihedral : 4.039 19.666 584 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.65 % Allowed : 17.44 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.36), residues: 536 helix: 2.18 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.42 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 196 TYR 0.017 0.001 TYR A 132 PHE 0.013 0.001 PHE A 309 TRP 0.022 0.001 TRP A 215 HIS 0.002 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 4396) covalent geometry : angle 0.48283 / 0.25 ( 5993) SS BOND : bond 0.00054 / 0.03 ( 1) SS BOND : angle 0.37149 / 0.20 ( 2) hydrogen bonds : bond 0.04389 / 2.84 ( 290) hydrogen bonds : angle 4.45597 / 3.11 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.156 Fit side-chains REVERT: A 116 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7700 (tttp) REVERT: A 164 GLU cc_start: 0.8041 (pm20) cc_final: 0.7753 (pm20) REVERT: A 167 LEU cc_start: 0.8069 (mt) cc_final: 0.7829 (mt) REVERT: A 212 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: A 214 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7242 (mmp-170) REVERT: A 278 GLN cc_start: 0.8442 (mt0) cc_final: 0.8157 (mt0) REVERT: A 413 ASP cc_start: 0.8352 (m-30) cc_final: 0.8086 (m-30) REVERT: A 444 ASP cc_start: 0.8884 (m-30) cc_final: 0.8632 (m-30) outliers start: 12 outliers final: 9 residues processed: 77 average time/residue: 0.3902 time to fit residues: 31.4369 Evaluate side-chains 81 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 525 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 52 optimal weight: 0.0980 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113876 restraints weight = 4900.110| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.56 r_work: 0.3320 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4397 Z= 0.117 Angle : 0.478 5.518 5995 Z= 0.244 Chirality : 0.037 0.139 674 Planarity : 0.004 0.043 726 Dihedral : 3.986 19.562 584 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.09 % Allowed : 17.00 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.36), residues: 536 helix: 2.22 (0.25), residues: 377 sheet: None (None), residues: 0 loop : -0.36 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.016 0.001 TYR A 132 PHE 0.014 0.001 PHE A 309 TRP 0.024 0.001 TRP A 215 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 4396) covalent geometry : angle 0.47800 / 0.24 ( 5993) SS BOND : bond 0.00028 / 0.01 ( 1) SS BOND : angle 0.25425 / 0.13 ( 2) hydrogen bonds : bond 0.04285 / 2.77 ( 290) hydrogen bonds : angle 4.40554 / 3.07 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.231 Fit side-chains REVERT: A 116 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7721 (tttp) REVERT: A 164 GLU cc_start: 0.8086 (pm20) cc_final: 0.7790 (pm20) REVERT: A 167 LEU cc_start: 0.8024 (mt) cc_final: 0.7819 (mt) REVERT: A 212 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: A 214 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7229 (mmp-170) REVERT: A 278 GLN cc_start: 0.8433 (mt0) cc_final: 0.8160 (mt0) REVERT: A 413 ASP cc_start: 0.8292 (m-30) cc_final: 0.8033 (m-30) REVERT: A 444 ASP cc_start: 0.8888 (m-30) cc_final: 0.8648 (m-30) outliers start: 14 outliers final: 9 residues processed: 78 average time/residue: 0.4441 time to fit residues: 36.1871 Evaluate side-chains 81 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 590 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111731 restraints weight = 4893.206| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.55 r_work: 0.3296 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4397 Z= 0.144 Angle : 0.509 5.763 5995 Z= 0.260 Chirality : 0.038 0.144 674 Planarity : 0.004 0.042 726 Dihedral : 4.113 19.801 584 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.65 % Allowed : 17.22 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.35), residues: 536 helix: 2.12 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.38 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 196 TYR 0.017 0.002 TYR A 132 PHE 0.013 0.001 PHE A 309 TRP 0.026 0.002 TRP A 215 HIS 0.002 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 4396) covalent geometry : angle 0.50874 / 0.26 ( 5993) SS BOND : bond 0.00008 / 0.00 ( 1) SS BOND : angle 0.28098 / 0.15 ( 2) hydrogen bonds : bond 0.04607 / 2.99 ( 290) hydrogen bonds : angle 4.53352 / 3.16 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1357.35 seconds wall clock time: 23 minutes 52.95 seconds (1432.95 seconds total)