Starting phenix.real_space_refine on Wed Jul 1 23:56:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hfi_34721/07_2026/8hfi_34721.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfi_34721/07_2026/8hfi_34721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hfi_34721/07_2026/8hfi_34721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfi_34721/07_2026/8hfi_34721.map" model { file = "/net/cci-nas-00/data/ceres_data/8hfi_34721/07_2026/8hfi_34721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfi_34721/07_2026/8hfi_34721.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.144 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 S 20 5.16 5 Cl 1 4.86 5 C 2963 2.51 5 N 681 2.21 5 O 778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4443 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4383 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 528} Chain breaks: 1 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 59 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'DSM': 1} Classifications: {'undetermined': 1, 'water': 39} Link IDs: {None: 38} Chain breaks: 1 Time building chain proxies: 1.13, per 1000 atoms: 0.25 Number of scatterers: 4443 At special positions: 0 Unit cell: (69.28, 68.1975, 97.425, 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) Cl 1 17.00 S 20 16.00 O 778 8.00 N 681 7.00 C 2963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " 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: 0.38 Conformation dependent library (CDL) restraints added in 124.3 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1008 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 1 sheets defined 83.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.552A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.518A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.623A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.520A pdb=" N GLY A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 262 through 283 removed outlier: 3.854A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 3.826A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.767A pdb=" N GLU A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 320 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.798A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Proline residue: A 392 - end of helix removed outlier: 3.705A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.659A pdb=" N GLY A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.613A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 496 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.594A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 592 Processing helix chain 'A' and resid 594 through 604 removed outlier: 3.790A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N HIS A 599 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 602 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 616 removed outlier: 3.813A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 299 hydrogen bonds defined for protein. 855 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: 0.70 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 647 1.30 - 1.43: 1376 1.43 - 1.55: 2493 1.55 - 1.68: 0 1.68 - 1.81: 31 Bond restraints: 4547 Sorted by residual: bond pdb=" C SER A 318 " pdb=" O SER A 318 " ideal model delta sigma weight residual 1.236 1.167 0.070 1.15e-02 7.56e+03 3.70e+01 bond pdb=" CA SER A 318 " pdb=" CB SER A 318 " ideal model delta sigma weight residual 1.529 1.457 0.072 1.55e-02 4.16e+03 2.13e+01 bond pdb=" N GLY A 60 " pdb=" CA GLY A 60 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.30e+00 bond pdb=" C5 DSM A 701 " pdb=" C6 DSM A 701 " ideal model delta sigma weight residual 1.524 1.549 -0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" CG1 ILE A 481 " pdb=" CD1 ILE A 481 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.38e+00 ... (remaining 4542 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 6113 2.08 - 4.17: 71 4.17 - 6.25: 10 6.25 - 8.33: 5 8.33 - 10.41: 3 Bond angle restraints: 6202 Sorted by residual: angle pdb=" C PHE A 317 " pdb=" N SER A 318 " pdb=" CA SER A 318 " ideal model delta sigma weight residual 120.44 127.79 -7.35 1.30e+00 5.92e-01 3.20e+01 angle pdb=" CA SER A 318 " pdb=" C SER A 318 " pdb=" O SER A 318 " ideal model delta sigma weight residual 120.82 116.52 4.30 1.05e+00 9.07e-01 1.67e+01 angle pdb=" C GLY A 106 " pdb=" N MET A 107 " pdb=" CA MET A 107 " ideal model delta sigma weight residual 119.78 114.75 5.03 1.24e+00 6.50e-01 1.64e+01 angle pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" C TYR A 205 " ideal model delta sigma weight residual 110.80 118.44 -7.64 2.13e+00 2.20e-01 1.29e+01 angle pdb=" C4 DSM A 701 " pdb=" C13 DSM A 701 " pdb=" C5 DSM A 701 " ideal model delta sigma weight residual 115.54 125.95 -10.41 3.00e+00 1.11e-01 1.20e+01 ... (remaining 6197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2242 17.44 - 34.87: 216 34.87 - 52.31: 65 52.31 - 69.74: 14 69.74 - 87.18: 2 Dihedral angle restraints: 2539 sinusoidal: 955 harmonic: 1584 Sorted by residual: dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual -180.00 -156.31 -23.69 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -132.79 10.19 0 2.50e+00 1.60e-01 1.66e+01 dihedral pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual 122.80 132.66 -9.86 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 2536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 670 0.091 - 0.181: 19 0.181 - 0.271: 0 0.271 - 0.362: 0 0.362 - 0.452: 1 Chirality restraints: 690 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CA ILE A 103 " pdb=" N ILE A 103 " pdb=" C ILE A 103 " pdb=" CB ILE A 103 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE A 606 " pdb=" N ILE A 606 " pdb=" C ILE A 606 " pdb=" CB ILE A 606 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 687 not shown) Planarity restraints: 752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C ILE A 103 " -0.070 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.027 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 318 " 0.016 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C SER A 318 " -0.058 2.00e-02 2.50e+03 pdb=" O SER A 318 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 319 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 DSM A 701 " -0.013 2.00e-02 2.50e+03 2.22e-02 9.86e+00 pdb=" C13 DSM A 701 " 0.010 2.00e-02 2.50e+03 pdb=" C14 DSM A 701 " -0.041 2.00e-02 2.50e+03 pdb=" C2 DSM A 701 " -0.000 2.00e-02 2.50e+03 pdb=" C3 DSM A 701 " 0.017 2.00e-02 2.50e+03 pdb=" C4 DSM A 701 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DSM A 701 " -0.014 2.00e-02 2.50e+03 pdb=" N1 DSM A 701 " 0.038 2.00e-02 2.50e+03 ... (remaining 749 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 33 2.59 - 3.16: 3814 3.16 - 3.74: 7288 3.74 - 4.32: 10368 4.32 - 4.90: 17016 Nonbonded interactions: 38519 Sorted by model distance: nonbonded pdb=" O HOH A 808 " pdb=" O HOH A 838 " model vdw 2.008 3.040 nonbonded pdb=" O HOH A 812 " pdb=" O HOH A 821 " model vdw 2.045 3.040 nonbonded pdb=" O PHE A 475 " pdb=" O HOH A 801 " model vdw 2.089 3.040 nonbonded pdb=" O ALA A 589 " pdb=" OG1 THR A 593 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR A 474 " pdb=" O HOH A 802 " model vdw 2.180 3.040 ... (remaining 38514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.840 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 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 : 0.003 0.072 4548 Z= 0.185 Angle : 0.628 10.413 6204 Z= 0.331 Chirality : 0.041 0.452 690 Planarity : 0.004 0.041 752 Dihedral : 15.560 87.178 1528 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.08 % Allowed : 16.23 % Favored : 82.68 % 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: 1.51 (0.38), residues: 544 helix: 1.42 (0.28), residues: 375 sheet: None (None), residues: 0 loop : 0.22 (0.53), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.013 0.001 TYR A 84 PHE 0.011 0.001 PHE A 409 TRP 0.007 0.001 TRP A 80 HIS 0.001 0.000 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.19 ( 4547) covalent geometry : angle 0.62831 / 0.33 ( 6202) SS BOND : bond 0.00338 / 0.21 ( 1) SS BOND : angle 0.69318 / 0.28 ( 2) hydrogen bonds : bond 0.13786 / 8.99 ( 299) hydrogen bonds : angle 5.50049 / 3.97 ( 855) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.143 Fit side-chains REVERT: A 488 GLU cc_start: 0.8457 (tt0) cc_final: 0.8223 (tt0) outliers start: 5 outliers final: 5 residues processed: 60 average time/residue: 0.3742 time to fit residues: 23.7173 Evaluate side-chains 56 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 396 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 HIS A 370 HIS A 375 ASN A 507 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.136799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113493 restraints weight = 5215.454| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.51 r_work: 0.3152 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4548 Z= 0.120 Angle : 0.559 8.173 6204 Z= 0.274 Chirality : 0.039 0.127 690 Planarity : 0.004 0.035 752 Dihedral : 7.327 61.164 605 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.73 % Allowed : 14.72 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.78 (0.37), residues: 544 helix: 1.52 (0.27), residues: 382 sheet: None (None), residues: 0 loop : 0.58 (0.54), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 518 TYR 0.015 0.001 TYR A 84 PHE 0.011 0.001 PHE A 110 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 4547) covalent geometry : angle 0.55868 / 0.27 ( 6202) SS BOND : bond 0.00248 / 0.16 ( 1) SS BOND : angle 0.72391 / 0.30 ( 2) hydrogen bonds : bond 0.04802 / 3.06 ( 299) hydrogen bonds : angle 4.57167 / 3.30 ( 855) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.131 Fit side-chains REVERT: A 242 MET cc_start: 0.8668 (mtp) cc_final: 0.8367 (mtp) REVERT: A 488 GLU cc_start: 0.8586 (tt0) cc_final: 0.8268 (tt0) REVERT: A 508 MET cc_start: 0.8761 (mtm) cc_final: 0.8255 (mtm) REVERT: A 515 LEU cc_start: 0.8940 (tp) cc_final: 0.8731 (tp) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 0.3244 time to fit residues: 22.3972 Evaluate side-chains 59 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 336 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113932 restraints weight = 5202.549| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.50 r_work: 0.2971 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4548 Z= 0.113 Angle : 0.529 8.380 6204 Z= 0.260 Chirality : 0.039 0.127 690 Planarity : 0.004 0.035 752 Dihedral : 7.250 64.525 602 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.73 % Allowed : 15.15 % Favored : 83.12 % 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: 1.94 (0.37), residues: 544 helix: 1.67 (0.27), residues: 383 sheet: None (None), residues: 0 loop : 0.53 (0.54), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 440 TYR 0.014 0.001 TYR A 84 PHE 0.010 0.001 PHE A 110 TRP 0.008 0.001 TRP A 553 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 4547) covalent geometry : angle 0.52881 / 0.26 ( 6202) SS BOND : bond 0.00252 / 0.16 ( 1) SS BOND : angle 0.69198 / 0.29 ( 2) hydrogen bonds : bond 0.04569 / 2.91 ( 299) hydrogen bonds : angle 4.42508 / 3.20 ( 855) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.196 Fit side-chains REVERT: A 242 MET cc_start: 0.8690 (mtp) cc_final: 0.8363 (mtp) REVERT: A 336 ASP cc_start: 0.8594 (p0) cc_final: 0.8345 (p0) REVERT: A 459 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7674 (t80) REVERT: A 488 GLU cc_start: 0.8611 (tt0) cc_final: 0.8279 (tt0) REVERT: A 508 MET cc_start: 0.8721 (mtm) cc_final: 0.8089 (mtm) REVERT: A 515 LEU cc_start: 0.8930 (tp) cc_final: 0.8691 (tp) outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 0.3524 time to fit residues: 22.7962 Evaluate side-chains 61 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 436 GLN A 507 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111547 restraints weight = 5113.377| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.50 r_work: 0.3092 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4548 Z= 0.130 Angle : 0.554 8.136 6204 Z= 0.275 Chirality : 0.040 0.132 690 Planarity : 0.004 0.036 752 Dihedral : 7.046 63.371 600 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.60 % Allowed : 15.37 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.37), residues: 544 helix: 1.57 (0.26), residues: 388 sheet: None (None), residues: 0 loop : 0.49 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 341 TYR 0.015 0.001 TYR A 84 PHE 0.014 0.001 PHE A 409 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 4547) covalent geometry : angle 0.55416 / 0.27 ( 6202) SS BOND : bond 0.00352 / 0.22 ( 1) SS BOND : angle 0.76283 / 0.31 ( 2) hydrogen bonds : bond 0.05168 / 3.29 ( 299) hydrogen bonds : angle 4.52517 / 3.26 ( 855) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.103 Fit side-chains REVERT: A 242 MET cc_start: 0.8756 (mtp) cc_final: 0.8413 (mtp) REVERT: A 336 ASP cc_start: 0.8555 (p0) cc_final: 0.8323 (p0) REVERT: A 488 GLU cc_start: 0.8638 (tt0) cc_final: 0.8383 (tt0) REVERT: A 515 LEU cc_start: 0.8942 (tp) cc_final: 0.8722 (tp) REVERT: A 581 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7379 (tp-100) outliers start: 12 outliers final: 5 residues processed: 62 average time/residue: 0.3413 time to fit residues: 22.3889 Evaluate side-chains 58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 581 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110524 restraints weight = 5169.831| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.50 r_work: 0.2911 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4548 Z= 0.140 Angle : 0.566 8.177 6204 Z= 0.281 Chirality : 0.041 0.136 690 Planarity : 0.004 0.037 752 Dihedral : 7.103 63.616 600 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.16 % Allowed : 16.23 % Favored : 81.60 % 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: 1.78 (0.37), residues: 544 helix: 1.56 (0.26), residues: 386 sheet: None (None), residues: 0 loop : 0.41 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 341 TYR 0.016 0.001 TYR A 84 PHE 0.014 0.002 PHE A 409 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 4547) covalent geometry : angle 0.56616 / 0.28 ( 6202) SS BOND : bond 0.00408 / 0.25 ( 1) SS BOND : angle 0.79473 / 0.31 ( 2) hydrogen bonds : bond 0.05387 / 3.42 ( 299) hydrogen bonds : angle 4.57201 / 3.29 ( 855) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.164 Fit side-chains REVERT: A 459 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7780 (t80) REVERT: A 488 GLU cc_start: 0.8731 (tt0) cc_final: 0.8487 (tt0) REVERT: A 515 LEU cc_start: 0.8934 (tp) cc_final: 0.8720 (tp) outliers start: 10 outliers final: 6 residues processed: 59 average time/residue: 0.3596 time to fit residues: 22.5229 Evaluate side-chains 59 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112317 restraints weight = 5262.018| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.52 r_work: 0.2922 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4548 Z= 0.123 Angle : 0.540 8.299 6204 Z= 0.267 Chirality : 0.040 0.131 690 Planarity : 0.004 0.035 752 Dihedral : 7.011 64.263 600 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.16 % Allowed : 16.23 % Favored : 81.60 % 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: 1.90 (0.37), residues: 544 helix: 1.68 (0.26), residues: 382 sheet: None (None), residues: 0 loop : 0.40 (0.54), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 81 TYR 0.017 0.001 TYR A 84 PHE 0.012 0.001 PHE A 323 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 4547) covalent geometry : angle 0.54019 / 0.27 ( 6202) SS BOND : bond 0.00329 / 0.21 ( 1) SS BOND : angle 0.72987 / 0.30 ( 2) hydrogen bonds : bond 0.04876 / 3.11 ( 299) hydrogen bonds : angle 4.47231 / 3.24 ( 855) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.216 Fit side-chains REVERT: A 459 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7765 (t80) REVERT: A 488 GLU cc_start: 0.8648 (tt0) cc_final: 0.8397 (tt0) REVERT: A 515 LEU cc_start: 0.8918 (tp) cc_final: 0.8688 (tp) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.3356 time to fit residues: 21.7841 Evaluate side-chains 59 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 481 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 9.9990 chunk 12 optimal weight: 0.0070 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 0.0020 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.6010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113685 restraints weight = 5200.079| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.51 r_work: 0.2984 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4548 Z= 0.114 Angle : 0.527 8.409 6204 Z= 0.260 Chirality : 0.039 0.129 690 Planarity : 0.004 0.034 752 Dihedral : 6.953 64.761 600 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.16 % Allowed : 16.02 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.37), residues: 544 helix: 1.73 (0.27), residues: 384 sheet: None (None), residues: 0 loop : 0.36 (0.55), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.016 0.001 TYR A 84 PHE 0.010 0.001 PHE A 323 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 4547) covalent geometry : angle 0.52681 / 0.26 ( 6202) SS BOND : bond 0.00290 / 0.18 ( 1) SS BOND : angle 0.71980 / 0.29 ( 2) hydrogen bonds : bond 0.04581 / 2.92 ( 299) hydrogen bonds : angle 4.40170 / 3.19 ( 855) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.147 Fit side-chains REVERT: A 459 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7775 (t80) REVERT: A 488 GLU cc_start: 0.8655 (tt0) cc_final: 0.8421 (tt0) REVERT: A 515 LEU cc_start: 0.8869 (tp) cc_final: 0.8589 (tp) outliers start: 10 outliers final: 5 residues processed: 60 average time/residue: 0.3523 time to fit residues: 22.4801 Evaluate side-chains 56 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.110045 restraints weight = 5168.924| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.51 r_work: 0.2908 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4548 Z= 0.150 Angle : 0.573 7.966 6204 Z= 0.286 Chirality : 0.042 0.138 690 Planarity : 0.004 0.035 752 Dihedral : 7.045 62.467 600 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.52 % Allowed : 16.45 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.37), residues: 544 helix: 1.57 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.44 (0.56), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 341 TYR 0.016 0.001 TYR A 84 PHE 0.016 0.002 PHE A 409 TRP 0.008 0.001 TRP A 553 HIS 0.003 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 4547) covalent geometry : angle 0.57327 / 0.29 ( 6202) SS BOND : bond 0.00459 / 0.29 ( 1) SS BOND : angle 0.84002 / 0.33 ( 2) hydrogen bonds : bond 0.05600 / 3.57 ( 299) hydrogen bonds : angle 4.58802 / 3.30 ( 855) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.147 Fit side-chains REVERT: A 488 GLU cc_start: 0.8717 (tt0) cc_final: 0.8364 (tt0) outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.2929 time to fit residues: 18.0803 Evaluate side-chains 56 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 444 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 HIS A 507 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.108564 restraints weight = 5192.977| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.51 r_work: 0.2934 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4548 Z= 0.174 Angle : 0.606 8.490 6204 Z= 0.304 Chirality : 0.043 0.143 690 Planarity : 0.004 0.037 752 Dihedral : 7.161 61.416 600 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.73 % Allowed : 17.10 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.37), residues: 544 helix: 1.45 (0.27), residues: 385 sheet: None (None), residues: 0 loop : 0.41 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 442 TYR 0.017 0.002 TYR A 84 PHE 0.017 0.002 PHE A 316 TRP 0.011 0.001 TRP A 517 HIS 0.003 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 ( 4547) covalent geometry : angle 0.60616 / 0.30 ( 6202) SS BOND : bond 0.00560 / 0.35 ( 1) SS BOND : angle 0.95471 / 0.37 ( 2) hydrogen bonds : bond 0.06102 / 3.87 ( 299) hydrogen bonds : angle 4.73210 / 3.39 ( 855) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.128 Fit side-chains REVERT: A 161 TYR cc_start: 0.8916 (t80) cc_final: 0.8587 (t80) REVERT: A 336 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8398 (p0) REVERT: A 488 GLU cc_start: 0.8767 (tt0) cc_final: 0.8533 (tt0) REVERT: A 515 LEU cc_start: 0.8970 (tp) cc_final: 0.8722 (tp) outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.3546 time to fit residues: 22.5018 Evaluate side-chains 59 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.134739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111194 restraints weight = 5169.074| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.51 r_work: 0.2977 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4548 Z= 0.128 Angle : 0.554 8.063 6204 Z= 0.275 Chirality : 0.040 0.133 690 Planarity : 0.004 0.036 752 Dihedral : 7.028 62.132 600 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.52 % Allowed : 17.53 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.37), residues: 544 helix: 1.62 (0.27), residues: 381 sheet: None (None), residues: 0 loop : 0.43 (0.55), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 518 TYR 0.017 0.001 TYR A 84 PHE 0.013 0.001 PHE A 409 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 4547) covalent geometry : angle 0.55392 / 0.27 ( 6202) SS BOND : bond 0.00357 / 0.22 ( 1) SS BOND : angle 0.82508 / 0.34 ( 2) hydrogen bonds : bond 0.05083 / 3.24 ( 299) hydrogen bonds : angle 4.53897 / 3.28 ( 855) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.162 Fit side-chains REVERT: A 336 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8393 (p0) REVERT: A 488 GLU cc_start: 0.8666 (tt0) cc_final: 0.8429 (tt0) REVERT: A 515 LEU cc_start: 0.8936 (tp) cc_final: 0.8720 (tp) outliers start: 7 outliers final: 5 residues processed: 58 average time/residue: 0.3275 time to fit residues: 20.1912 Evaluate side-chains 56 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 39 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111992 restraints weight = 5166.280| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.51 r_work: 0.2985 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4548 Z= 0.124 Angle : 0.554 9.636 6204 Z= 0.272 Chirality : 0.040 0.129 690 Planarity : 0.004 0.035 752 Dihedral : 6.977 62.267 600 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.73 % Allowed : 17.32 % Favored : 80.95 % 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: 1.87 (0.37), residues: 544 helix: 1.67 (0.27), residues: 382 sheet: None (None), residues: 0 loop : 0.37 (0.55), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 518 TYR 0.019 0.001 TYR A 391 PHE 0.013 0.001 PHE A 409 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 4547) covalent geometry : angle 0.55341 / 0.27 ( 6202) SS BOND : bond 0.00326 / 0.20 ( 1) SS BOND : angle 0.86394 / 0.36 ( 2) hydrogen bonds : bond 0.04909 / 3.13 ( 299) hydrogen bonds : angle 4.47787 / 3.24 ( 855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1512.04 seconds wall clock time: 26 minutes 34.22 seconds (1594.22 seconds total)