Starting phenix.real_space_refine on Fri Aug 22 14:50:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hfi_34721/08_2025/8hfi_34721.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfi_34721/08_2025/8hfi_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_34721/08_2025/8hfi_34721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfi_34721/08_2025/8hfi_34721.map" model { file = "/net/cci-nas-00/data/ceres_data/8hfi_34721/08_2025/8hfi_34721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfi_34721/08_2025/8hfi_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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, 60 Unusual residues: {' CL': 1, 'DSM': 1} Classifications: {'undetermined': 2, 'water': 39} Link IDs: {None: 40} Time building chain proxies: 1.43, per 1000 atoms: 0.32 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: 0.39 Conformation dependent library (CDL) restraints added in 174.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.16 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: 0.71 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: 1.17 - 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: 0.560 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.550 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 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 aren 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 covalent geometry : bond 0.00340 ( 4547) covalent geometry : angle 0.62831 ( 6202) SS BOND : bond 0.00338 ( 1) SS BOND : angle 0.69318 ( 2) hydrogen bonds : bond 0.13786 ( 299) hydrogen bonds : angle 5.50049 ( 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 : 0.192 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: 0.4056 time to fit residues: 25.6980 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 : 0.166 ------------------------------------------------------------------------------- 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: 0.7980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 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... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 375 ASN A 507 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113314 restraints weight = 5211.537| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.51 r_work: 0.2978 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4548 Z= 0.121 Angle : 0.560 8.055 6204 Z= 0.275 Chirality : 0.039 0.127 690 Planarity : 0.004 0.035 752 Dihedral : 7.342 61.469 605 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.96 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 aren 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 : 0.57 (0.54), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 442 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 covalent geometry : bond 0.00258 ( 4547) covalent geometry : angle 0.55961 ( 6202) SS BOND : bond 0.00255 ( 1) SS BOND : angle 0.72302 ( 2) hydrogen bonds : bond 0.04866 ( 299) hydrogen bonds : angle 4.57412 ( 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 69 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.178 Fit side-chains REVERT: A 242 MET cc_start: 0.8640 (mtp) cc_final: 0.8342 (mtp) REVERT: A 488 GLU cc_start: 0.8630 (tt0) cc_final: 0.8314 (tt0) REVERT: A 508 MET cc_start: 0.8713 (mtm) cc_final: 0.8176 (mtm) REVERT: A 515 LEU cc_start: 0.8934 (tp) cc_final: 0.8732 (tp) outliers start: 8 outliers final: 4 residues processed: 66 average time/residue: 0.3492 time to fit residues: 24.5672 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 : 0.147 ------------------------------------------------------------------------------- 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: 0.6980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 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 = 0.3596 r_free = 0.3596 target = 0.135374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111957 restraints weight = 5186.854| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.50 r_work: 0.2964 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4548 Z= 0.125 Angle : 0.550 8.132 6204 Z= 0.272 Chirality : 0.040 0.130 690 Planarity : 0.004 0.035 752 Dihedral : 7.318 63.441 602 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.95 % Allowed : 15.15 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.37), residues: 544 helix: 1.61 (0.27), residues: 383 sheet: None (None), residues: 0 loop : 0.50 (0.54), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 442 TYR 0.014 0.001 TYR A 84 PHE 0.012 0.001 PHE A 409 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4547) covalent geometry : angle 0.54989 ( 6202) SS BOND : bond 0.00318 ( 1) SS BOND : angle 0.74536 ( 2) hydrogen bonds : bond 0.05020 ( 299) hydrogen bonds : angle 4.52108 ( 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 67 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.179 Fit side-chains REVERT: A 242 MET cc_start: 0.8715 (mtp) cc_final: 0.8383 (mtp) REVERT: A 336 ASP cc_start: 0.8614 (p0) cc_final: 0.8367 (p0) REVERT: A 459 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7719 (t80) REVERT: A 488 GLU cc_start: 0.8633 (tt0) cc_final: 0.8298 (tt0) REVERT: A 508 MET cc_start: 0.8720 (mtm) cc_final: 0.8219 (mtm) REVERT: A 515 LEU cc_start: 0.8941 (tp) cc_final: 0.8716 (tp) outliers start: 9 outliers final: 5 residues processed: 63 average time/residue: 0.3615 time to fit residues: 24.2302 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 : 0.163 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 0.0970 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.132882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109395 restraints weight = 5098.756| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.49 r_work: 0.2901 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4548 Z= 0.153 Angle : 0.588 8.117 6204 Z= 0.293 Chirality : 0.042 0.139 690 Planarity : 0.005 0.038 752 Dihedral : 7.163 62.521 600 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.73 % Allowed : 16.02 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.37), residues: 544 helix: 1.50 (0.26), residues: 386 sheet: None (None), residues: 0 loop : 0.42 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 442 TYR 0.017 0.001 TYR A 391 PHE 0.014 0.002 PHE A 409 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 4547) covalent geometry : angle 0.58765 ( 6202) SS BOND : bond 0.00455 ( 1) SS BOND : angle 0.87087 ( 2) hydrogen bonds : bond 0.05761 ( 299) hydrogen bonds : angle 4.67108 ( 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 63 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.196 Fit side-chains REVERT: A 242 MET cc_start: 0.8736 (mtp) cc_final: 0.8392 (mtp) REVERT: A 488 GLU cc_start: 0.8750 (tt0) cc_final: 0.8423 (tt0) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.3692 time to fit residues: 23.1904 Evaluate side-chains 60 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 52 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.109843 restraints weight = 5171.090| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.49 r_work: 0.2893 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4548 Z= 0.148 Angle : 0.575 8.051 6204 Z= 0.287 Chirality : 0.041 0.137 690 Planarity : 0.005 0.038 752 Dihedral : 7.145 63.314 600 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.38 % Allowed : 15.58 % 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 aren not related in a simple way. whole: 1.69 (0.37), residues: 544 helix: 1.50 (0.26), residues: 385 sheet: None (None), residues: 0 loop : 0.38 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 442 TYR 0.017 0.001 TYR A 84 PHE 0.014 0.002 PHE A 409 TRP 0.009 0.001 TRP A 517 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4547) covalent geometry : angle 0.57481 ( 6202) SS BOND : bond 0.00427 ( 1) SS BOND : angle 0.86406 ( 2) hydrogen bonds : bond 0.05507 ( 299) hydrogen bonds : angle 4.63562 ( 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: 11 poor density : 53 time to evaluate : 0.167 Fit side-chains REVERT: A 336 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8377 (p0) REVERT: A 488 GLU cc_start: 0.8730 (tt0) cc_final: 0.8394 (tt0) REVERT: A 515 LEU cc_start: 0.8952 (tp) cc_final: 0.8722 (tp) outliers start: 11 outliers final: 6 residues processed: 62 average time/residue: 0.3550 time to fit residues: 23.4510 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 : 0.193 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 481 ILE 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: 4.9990 chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111631 restraints weight = 5250.611| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.51 r_work: 0.2928 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1370 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= 0.126 Angle : 0.548 8.209 6204 Z= 0.271 Chirality : 0.040 0.131 690 Planarity : 0.004 0.037 752 Dihedral : 7.055 63.613 600 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.81 % Allowed : 15.37 % 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 aren not related in a simple way. whole: 1.88 (0.37), residues: 544 helix: 1.66 (0.27), residues: 381 sheet: None (None), residues: 0 loop : 0.41 (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 covalent geometry : bond 0.00281 ( 4547) covalent geometry : angle 0.54765 ( 6202) SS BOND : bond 0.00332 ( 1) SS BOND : angle 0.80017 ( 2) hydrogen bonds : bond 0.04987 ( 299) hydrogen bonds : angle 4.51014 ( 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 66 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.162 Fit side-chains REVERT: A 242 MET cc_start: 0.8722 (mtp) cc_final: 0.8438 (mtp) REVERT: A 336 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8364 (p0) REVERT: A 459 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7702 (t80) REVERT: A 488 GLU cc_start: 0.8659 (tt0) cc_final: 0.8326 (tt0) REVERT: A 515 LEU cc_start: 0.8958 (tp) cc_final: 0.8719 (tp) outliers start: 13 outliers final: 8 residues processed: 62 average time/residue: 0.3624 time to fit residues: 23.9236 Evaluate side-chains 63 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 373 LYS 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: 0.4980 chunk 12 optimal weight: 0.0980 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 0.0670 chunk 49 optimal weight: 0.8980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.115895 restraints weight = 5205.722| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.50 r_work: 0.3161 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4548 Z= 0.104 Angle : 0.510 8.570 6204 Z= 0.250 Chirality : 0.038 0.123 690 Planarity : 0.004 0.035 752 Dihedral : 6.906 65.375 600 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.38 % Allowed : 16.02 % 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 aren not related in a simple way. whole: 2.04 (0.38), residues: 544 helix: 1.78 (0.27), residues: 385 sheet: None (None), residues: 0 loop : 0.44 (0.56), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 518 TYR 0.016 0.001 TYR A 84 PHE 0.009 0.001 PHE A 323 TRP 0.009 0.001 TRP A 235 HIS 0.001 0.000 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 4547) covalent geometry : angle 0.50977 ( 6202) SS BOND : bond 0.00213 ( 1) SS BOND : angle 0.68482 ( 2) hydrogen bonds : bond 0.04151 ( 299) hydrogen bonds : angle 4.33186 ( 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 67 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.177 Fit side-chains REVERT: A 336 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8350 (p0) REVERT: A 459 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7660 (t80) REVERT: A 488 GLU cc_start: 0.8615 (tt0) cc_final: 0.8296 (tt0) REVERT: A 515 LEU cc_start: 0.8944 (tp) cc_final: 0.8735 (tp) outliers start: 11 outliers final: 6 residues processed: 65 average time/residue: 0.3639 time to fit residues: 25.1459 Evaluate side-chains 60 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113971 restraints weight = 5176.090| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.51 r_work: 0.3013 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4548 Z= 0.112 Angle : 0.527 8.443 6204 Z= 0.258 Chirality : 0.039 0.128 690 Planarity : 0.004 0.034 752 Dihedral : 6.920 64.802 600 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.95 % Allowed : 17.10 % 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 aren not related in a simple way. whole: 1.95 (0.37), residues: 544 helix: 1.72 (0.27), residues: 389 sheet: None (None), residues: 0 loop : 0.38 (0.56), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.016 0.001 TYR A 391 PHE 0.010 0.001 PHE A 110 TRP 0.009 0.001 TRP A 553 HIS 0.001 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 4547) covalent geometry : angle 0.52667 ( 6202) SS BOND : bond 0.00282 ( 1) SS BOND : angle 0.75873 ( 2) hydrogen bonds : bond 0.04550 ( 299) hydrogen bonds : angle 4.37386 ( 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 61 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.158 Fit side-chains REVERT: A 459 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7720 (t80) REVERT: A 488 GLU cc_start: 0.8699 (tt0) cc_final: 0.8469 (tt0) REVERT: A 515 LEU cc_start: 0.8942 (tp) cc_final: 0.8722 (tp) outliers start: 9 outliers final: 6 residues processed: 59 average time/residue: 0.3409 time to fit residues: 21.4874 Evaluate side-chains 58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 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: 0.8980 chunk 15 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110087 restraints weight = 5186.060| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.50 r_work: 0.2925 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1516 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= 0.148 Angle : 0.574 8.000 6204 Z= 0.286 Chirality : 0.042 0.139 690 Planarity : 0.004 0.036 752 Dihedral : 7.051 62.522 600 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.52 % Allowed : 17.75 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.37), residues: 544 helix: 1.61 (0.26), residues: 386 sheet: None (None), residues: 0 loop : 0.40 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 341 TYR 0.021 0.001 TYR A 391 PHE 0.015 0.002 PHE A 409 TRP 0.009 0.001 TRP A 517 HIS 0.003 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4547) covalent geometry : angle 0.57412 ( 6202) SS BOND : bond 0.00456 ( 1) SS BOND : angle 0.87450 ( 2) hydrogen bonds : bond 0.05569 ( 299) hydrogen bonds : angle 4.57135 ( 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 59 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.178 Fit side-chains REVERT: A 336 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8425 (p0) REVERT: A 488 GLU cc_start: 0.8696 (tt0) cc_final: 0.8431 (tt0) REVERT: A 515 LEU cc_start: 0.8946 (tp) cc_final: 0.8687 (tp) outliers start: 7 outliers final: 6 residues processed: 57 average time/residue: 0.3551 time to fit residues: 21.6316 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 : 0.179 ------------------------------------------------------------------------------- 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: 10.0000 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.0010 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111418 restraints weight = 5157.520| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.50 r_work: 0.2949 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4548 Z= 0.130 Angle : 0.553 8.023 6204 Z= 0.274 Chirality : 0.041 0.134 690 Planarity : 0.004 0.035 752 Dihedral : 7.013 62.276 600 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.52 % Allowed : 17.75 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.37), residues: 544 helix: 1.63 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.40 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 341 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 covalent geometry : bond 0.00290 ( 4547) covalent geometry : angle 0.55281 ( 6202) SS BOND : bond 0.00371 ( 1) SS BOND : angle 0.84572 ( 2) hydrogen bonds : bond 0.05101 ( 299) hydrogen bonds : angle 4.49817 ( 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 57 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.165 Fit side-chains REVERT: A 242 MET cc_start: 0.8739 (mtp) cc_final: 0.8484 (mtp) REVERT: A 336 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8414 (p0) REVERT: A 488 GLU cc_start: 0.8683 (tt0) cc_final: 0.8472 (tt0) outliers start: 7 outliers final: 6 residues processed: 56 average time/residue: 0.3698 time to fit residues: 22.0654 Evaluate side-chains 57 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 17 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112478 restraints weight = 5150.748| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.49 r_work: 0.2992 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4548 Z= 0.122 Angle : 0.542 8.086 6204 Z= 0.268 Chirality : 0.040 0.129 690 Planarity : 0.004 0.035 752 Dihedral : 6.966 62.407 600 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.52 % Allowed : 18.18 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.37), residues: 544 helix: 1.64 (0.27), residues: 387 sheet: None (None), residues: 0 loop : 0.35 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 518 TYR 0.018 0.001 TYR A 391 PHE 0.011 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 covalent geometry : bond 0.00265 ( 4547) covalent geometry : angle 0.54164 ( 6202) SS BOND : bond 0.00341 ( 1) SS BOND : angle 0.91452 ( 2) hydrogen bonds : bond 0.04880 ( 299) hydrogen bonds : angle 4.44469 ( 855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1582.26 seconds wall clock time: 27 minutes 50.93 seconds (1670.93 seconds total)