Starting phenix.real_space_refine on Thu Sep 18 05:33:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lys_23600/09_2025/7lys_23600.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lys_23600/09_2025/7lys_23600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lys_23600/09_2025/7lys_23600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lys_23600/09_2025/7lys_23600.map" model { file = "/net/cci-nas-00/data/ceres_data/7lys_23600/09_2025/7lys_23600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lys_23600/09_2025/7lys_23600.cif" } resolution = 3.05 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= 0.171 sd= 1.109 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 899 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 88 5.49 5 S 14 5.16 5 C 4232 2.51 5 N 1313 2.21 5 O 1552 1.98 5 H 6374 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13573 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 10734 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 39, 'TRANS': 629} Chain breaks: 2 Chain: "B" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 1323 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 35} Chain: "C" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 948 Classifications: {'DNA': 30} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 568 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Time building chain proxies: 2.68, per 1000 atoms: 0.20 Number of scatterers: 13573 At special positions: 0 Unit cell: (84.74, 99.235, 125.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 88 15.00 O 1552 8.00 N 1313 7.00 C 4232 6.00 H 6374 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.21 Conformation dependent library (CDL) restraints added in 329.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1266 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 48.7% alpha, 9.4% beta 31 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 24 through 39 Processing helix chain 'A' and resid 40 through 48 removed outlier: 4.311A pdb=" N VAL A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 93 through 99 Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 125 through 169 removed outlier: 3.648A pdb=" N LEU A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.740A pdb=" N ARG A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 373 through 384 removed outlier: 4.194A pdb=" N ALA A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 453 removed outlier: 3.838A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 483 removed outlier: 5.461A pdb=" N LYS A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 549 through 566 Processing helix chain 'A' and resid 568 through 597 removed outlier: 3.531A pdb=" N LYS A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 636 through 651 removed outlier: 4.347A pdb=" N THR A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 708 Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 199 removed outlier: 5.741A pdb=" N VAL A 66 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASP A 312 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 262 Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 371 removed outlier: 6.313A pdb=" N LEU A 370 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 391 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 606 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU A 395 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 388 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG A 407 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA5, first strand: chain 'A' and resid 516 through 517 removed outlier: 3.562A pdb=" N VAL A 533 " --> pdb=" O PHE A 517 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6365 1.03 - 1.23: 51 1.23 - 1.42: 3348 1.42 - 1.62: 4126 1.62 - 1.81: 19 Bond restraints: 13909 Sorted by residual: bond pdb=" C3' DC D -9 " pdb=" O3' DC D -9 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.55e+00 bond pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " ideal model delta sigma weight residual 1.422 1.451 -0.029 3.00e-02 1.11e+03 9.41e-01 bond pdb=" O4' DC C 3 " pdb=" C1' DC C 3 " ideal model delta sigma weight residual 1.414 1.399 0.015 2.00e-02 2.50e+03 5.65e-01 bond pdb=" O4' DT D -5 " pdb=" C1' DT D -5 " ideal model delta sigma weight residual 1.414 1.399 0.015 2.00e-02 2.50e+03 5.57e-01 bond pdb=" CB ARG A 488 " pdb=" CG ARG A 488 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.15e-01 ... (remaining 13904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 21788 0.83 - 1.66: 2786 1.66 - 2.48: 432 2.48 - 3.31: 127 3.31 - 4.14: 14 Bond angle restraints: 25147 Sorted by residual: angle pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " pdb=" C1' DG D -8 " ideal model delta sigma weight residual 101.60 105.07 -3.47 1.50e+00 4.44e-01 5.35e+00 angle pdb=" C3' DC D 5 " pdb=" C2' DC D 5 " pdb=" C1' DC D 5 " ideal model delta sigma weight residual 101.60 104.72 -3.12 1.50e+00 4.44e-01 4.33e+00 angle pdb=" C4' DC D -9 " pdb=" C3' DC D -9 " pdb=" O3' DC D -9 " ideal model delta sigma weight residual 110.00 113.04 -3.04 1.50e+00 4.44e-01 4.11e+00 angle pdb=" C4' DG D -8 " pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " ideal model delta sigma weight residual 102.40 105.03 -2.63 1.50e+00 4.44e-01 3.08e+00 angle pdb=" C3' DT C -8 " pdb=" C2' DT C -8 " pdb=" C1' DT C -8 " ideal model delta sigma weight residual 101.60 104.10 -2.50 1.50e+00 4.44e-01 2.79e+00 ... (remaining 25142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.78: 5952 33.78 - 67.57: 436 67.57 - 101.35: 20 101.35 - 135.13: 0 135.13 - 168.92: 2 Dihedral angle restraints: 6410 sinusoidal: 4152 harmonic: 2258 Sorted by residual: dihedral pdb=" CA PRO A 171 " pdb=" C PRO A 171 " pdb=" N GLU A 172 " pdb=" CA GLU A 172 " ideal model delta harmonic sigma weight residual -180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA VAL A 236 " pdb=" C VAL A 236 " pdb=" N VAL A 237 " pdb=" CA VAL A 237 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PHE A 653 " pdb=" C PHE A 653 " pdb=" N TYR A 654 " pdb=" CA TYR A 654 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 6407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 779 0.029 - 0.058: 297 0.058 - 0.087: 62 0.087 - 0.117: 61 0.117 - 0.146: 8 Chirality restraints: 1207 Sorted by residual: chirality pdb=" CA ILE A 262 " pdb=" N ILE A 262 " pdb=" C ILE A 262 " pdb=" CB ILE A 262 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE A 330 " pdb=" N ILE A 330 " pdb=" C ILE A 330 " pdb=" CB ILE A 330 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA VAL A 302 " pdb=" N VAL A 302 " pdb=" C VAL A 302 " pdb=" CB VAL A 302 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1204 not shown) Planarity restraints: 1746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 620 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 621 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 60 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.09e-01 pdb=" N PRO A 61 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 614 " 0.007 2.00e-02 2.50e+03 6.11e-03 8.39e-01 pdb=" CG HIS A 614 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 614 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS A 614 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 614 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 614 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 HIS A 614 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 HIS A 614 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS A 614 " -0.001 2.00e-02 2.50e+03 ... (remaining 1743 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 815 2.20 - 2.80: 25702 2.80 - 3.40: 35520 3.40 - 4.00: 47770 4.00 - 4.60: 71518 Nonbonded interactions: 181325 Sorted by model distance: nonbonded pdb=" OD1 ASN A 183 " pdb=" H GLU A 184 " model vdw 1.596 2.450 nonbonded pdb=" OE1 GLN A 386 " pdb=" H GLN A 386 " model vdw 1.625 2.450 nonbonded pdb="HH12 ARG A 582 " pdb=" OP2 G B 2 " model vdw 1.626 2.450 nonbonded pdb=" HZ1 LYS A 536 " pdb=" O5' DG C -18 " model vdw 1.636 2.450 nonbonded pdb=" HH TYR A 123 " pdb=" OH TYR A 201 " model vdw 1.679 2.450 ... (remaining 181320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.080 Extract box with map and model: 0.180 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 15.220 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 0.039 7535 Z= 0.163 Angle : 0.540 4.141 10601 Z= 0.315 Chirality : 0.038 0.146 1207 Planarity : 0.003 0.032 1048 Dihedral : 20.021 168.916 3244 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 5.93 % Favored : 93.89 % 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: -1.46 (0.30), residues: 663 helix: -0.22 (0.29), residues: 295 sheet: -1.50 (0.55), residues: 74 loop : -1.52 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 538 TYR 0.010 0.001 TYR A 201 PHE 0.015 0.001 PHE A 613 TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 7535) covalent geometry : angle 0.54014 (10601) hydrogen bonds : bond 0.21570 ( 344) hydrogen bonds : angle 7.08980 ( 910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 ILE cc_start: 0.9280 (mm) cc_final: 0.9040 (mt) REVERT: A 659 ARG cc_start: 0.8510 (mtt-85) cc_final: 0.8245 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.2567 time to fit residues: 29.8416 Evaluate side-chains 76 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.0170 chunk 27 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3136 r_free = 0.3136 target = 0.076739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.066998 restraints weight = 43592.896| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.70 r_work: 0.2850 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7535 Z= 0.145 Angle : 0.555 3.835 10601 Z= 0.313 Chirality : 0.039 0.152 1207 Planarity : 0.004 0.036 1048 Dihedral : 21.679 169.079 1908 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.17 % Allowed : 9.77 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.32), residues: 663 helix: 0.84 (0.30), residues: 303 sheet: -1.30 (0.58), residues: 74 loop : -0.98 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.009 0.001 TYR A 654 PHE 0.017 0.001 PHE A 613 TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7535) covalent geometry : angle 0.55546 (10601) hydrogen bonds : bond 0.05161 ( 344) hydrogen bonds : angle 4.71656 ( 910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8659 (ttm170) cc_final: 0.8303 (mtt-85) REVERT: A 659 ARG cc_start: 0.8502 (mtt-85) cc_final: 0.8254 (mtt-85) outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.3187 time to fit residues: 30.7805 Evaluate side-chains 74 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3127 r_free = 0.3127 target = 0.076241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.066474 restraints weight = 43948.878| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.69 r_work: 0.2843 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7535 Z= 0.157 Angle : 0.540 5.287 10601 Z= 0.302 Chirality : 0.039 0.140 1207 Planarity : 0.004 0.051 1048 Dihedral : 21.609 170.970 1908 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.52 % Allowed : 10.99 % Favored : 88.48 % 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: 0.12 (0.33), residues: 663 helix: 1.37 (0.31), residues: 305 sheet: -1.64 (0.56), residues: 79 loop : -0.80 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 488 TYR 0.009 0.001 TYR A 654 PHE 0.015 0.001 PHE A 354 TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7535) covalent geometry : angle 0.53979 (10601) hydrogen bonds : bond 0.04593 ( 344) hydrogen bonds : angle 4.36397 ( 910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8694 (ttm170) cc_final: 0.8399 (mtt-85) REVERT: A 659 ARG cc_start: 0.8553 (mtt-85) cc_final: 0.8292 (mtt-85) outliers start: 3 outliers final: 3 residues processed: 76 average time/residue: 0.3032 time to fit residues: 28.2139 Evaluate side-chains 76 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 10 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 0.0270 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- 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 = 0.3135 r_free = 0.3135 target = 0.076619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.066947 restraints weight = 43248.778| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.69 r_work: 0.2852 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7535 Z= 0.170 Angle : 0.536 4.853 10601 Z= 0.300 Chirality : 0.039 0.141 1207 Planarity : 0.004 0.035 1048 Dihedral : 21.550 169.946 1908 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.87 % Allowed : 12.91 % Favored : 86.21 % 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: 0.38 (0.34), residues: 663 helix: 1.63 (0.31), residues: 306 sheet: -1.62 (0.56), residues: 74 loop : -0.71 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 547 TYR 0.009 0.001 TYR A 654 PHE 0.015 0.001 PHE A 354 TRP 0.005 0.001 TRP A 308 HIS 0.007 0.002 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7535) covalent geometry : angle 0.53585 (10601) hydrogen bonds : bond 0.04197 ( 344) hydrogen bonds : angle 4.14995 ( 910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8338 (tp) REVERT: A 204 ILE cc_start: 0.8387 (mm) cc_final: 0.7944 (pt) REVERT: A 284 ARG cc_start: 0.8748 (ttm170) cc_final: 0.8447 (mtt-85) REVERT: A 295 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8685 (mm-40) outliers start: 5 outliers final: 4 residues processed: 79 average time/residue: 0.2928 time to fit residues: 28.2198 Evaluate side-chains 76 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.077794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.068122 restraints weight = 43388.906| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.66 r_work: 0.2873 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7535 Z= 0.130 Angle : 0.513 3.970 10601 Z= 0.288 Chirality : 0.038 0.140 1207 Planarity : 0.004 0.036 1048 Dihedral : 21.515 170.148 1908 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.52 % Allowed : 13.79 % Favored : 85.69 % 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: 0.58 (0.34), residues: 663 helix: 1.78 (0.31), residues: 306 sheet: -1.66 (0.54), residues: 74 loop : -0.54 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 155 TYR 0.009 0.001 TYR A 654 PHE 0.015 0.001 PHE A 354 TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7535) covalent geometry : angle 0.51320 (10601) hydrogen bonds : bond 0.03965 ( 344) hydrogen bonds : angle 4.04795 ( 910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8287 (tp) REVERT: A 139 ARG cc_start: 0.8825 (mtm-85) cc_final: 0.8552 (mtm-85) REVERT: A 204 ILE cc_start: 0.8313 (mm) cc_final: 0.7891 (pt) REVERT: A 284 ARG cc_start: 0.8717 (ttm170) cc_final: 0.8406 (mtt-85) outliers start: 3 outliers final: 2 residues processed: 77 average time/residue: 0.2702 time to fit residues: 25.9577 Evaluate side-chains 75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 325 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 61 optimal weight: 0.0670 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- 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 = 0.3098 r_free = 0.3098 target = 0.074606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.065044 restraints weight = 43642.489| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.67 r_work: 0.2814 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7535 Z= 0.242 Angle : 0.569 4.228 10601 Z= 0.317 Chirality : 0.042 0.142 1207 Planarity : 0.005 0.035 1048 Dihedral : 21.534 169.288 1908 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.40 % Allowed : 13.44 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.34), residues: 663 helix: 1.74 (0.31), residues: 305 sheet: -1.88 (0.53), residues: 74 loop : -0.60 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 139 TYR 0.011 0.001 TYR A 654 PHE 0.015 0.001 PHE A 613 TRP 0.005 0.001 TRP A 308 HIS 0.007 0.002 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 7535) covalent geometry : angle 0.56929 (10601) hydrogen bonds : bond 0.04411 ( 344) hydrogen bonds : angle 4.08257 ( 910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8295 (tp) REVERT: A 204 ILE cc_start: 0.8491 (mm) cc_final: 0.8119 (pt) REVERT: A 284 ARG cc_start: 0.8768 (ttm170) cc_final: 0.8453 (mtt-85) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.2630 time to fit residues: 26.0139 Evaluate side-chains 79 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3119 r_free = 0.3119 target = 0.075738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.066135 restraints weight = 43203.204| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.66 r_work: 0.2833 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7535 Z= 0.174 Angle : 0.537 4.173 10601 Z= 0.300 Chirality : 0.039 0.137 1207 Planarity : 0.004 0.034 1048 Dihedral : 21.525 169.481 1908 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.22 % Allowed : 13.61 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.34), residues: 663 helix: 1.81 (0.31), residues: 305 sheet: -1.88 (0.53), residues: 74 loop : -0.56 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 155 TYR 0.010 0.001 TYR A 654 PHE 0.015 0.001 PHE A 354 TRP 0.006 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 7535) covalent geometry : angle 0.53737 (10601) hydrogen bonds : bond 0.04120 ( 344) hydrogen bonds : angle 4.03341 ( 910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8835 (mtm-85) cc_final: 0.8545 (mtm-85) REVERT: A 204 ILE cc_start: 0.8453 (mm) cc_final: 0.8080 (pt) REVERT: A 284 ARG cc_start: 0.8734 (ttm170) cc_final: 0.8426 (mtt-85) outliers start: 7 outliers final: 7 residues processed: 77 average time/residue: 0.2777 time to fit residues: 26.5389 Evaluate side-chains 77 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.075239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.065745 restraints weight = 43116.064| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.65 r_work: 0.2828 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7535 Z= 0.190 Angle : 0.542 4.183 10601 Z= 0.302 Chirality : 0.040 0.136 1207 Planarity : 0.004 0.036 1048 Dihedral : 21.505 169.205 1908 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.22 % Allowed : 13.96 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.34), residues: 663 helix: 1.83 (0.31), residues: 305 sheet: -1.53 (0.55), residues: 64 loop : -0.66 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 155 TYR 0.011 0.001 TYR A 654 PHE 0.012 0.001 PHE A 613 TRP 0.006 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 7535) covalent geometry : angle 0.54201 (10601) hydrogen bonds : bond 0.04124 ( 344) hydrogen bonds : angle 4.01982 ( 910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8830 (mtm-85) cc_final: 0.8549 (mtm-85) REVERT: A 204 ILE cc_start: 0.8507 (mm) cc_final: 0.8173 (pt) REVERT: A 284 ARG cc_start: 0.8740 (ttm170) cc_final: 0.8446 (mtt-85) outliers start: 7 outliers final: 7 residues processed: 78 average time/residue: 0.2607 time to fit residues: 25.3170 Evaluate side-chains 79 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3140 r_free = 0.3140 target = 0.076839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.067228 restraints weight = 43369.554| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.64 r_work: 0.2855 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7535 Z= 0.136 Angle : 0.519 4.235 10601 Z= 0.290 Chirality : 0.038 0.137 1207 Planarity : 0.004 0.037 1048 Dihedral : 21.457 169.147 1908 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.87 % Allowed : 14.31 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.34), residues: 663 helix: 1.97 (0.31), residues: 305 sheet: -1.47 (0.55), residues: 64 loop : -0.60 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 155 TYR 0.010 0.001 TYR A 654 PHE 0.013 0.001 PHE A 354 TRP 0.008 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7535) covalent geometry : angle 0.51907 (10601) hydrogen bonds : bond 0.03862 ( 344) hydrogen bonds : angle 3.93336 ( 910) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8809 (mtm-85) cc_final: 0.8550 (mtm-85) REVERT: A 204 ILE cc_start: 0.8437 (mm) cc_final: 0.8118 (pt) REVERT: A 284 ARG cc_start: 0.8714 (ttm170) cc_final: 0.8412 (mtt-85) outliers start: 5 outliers final: 5 residues processed: 82 average time/residue: 0.2733 time to fit residues: 27.3774 Evaluate side-chains 77 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 18 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3153 r_free = 0.3153 target = 0.077572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.067944 restraints weight = 42968.897| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.64 r_work: 0.2870 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7535 Z= 0.131 Angle : 0.513 4.300 10601 Z= 0.287 Chirality : 0.038 0.135 1207 Planarity : 0.004 0.039 1048 Dihedral : 21.377 168.898 1908 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.87 % Allowed : 14.83 % Favored : 84.29 % 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: 0.89 (0.34), residues: 663 helix: 2.09 (0.31), residues: 304 sheet: -1.30 (0.56), residues: 64 loop : -0.54 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 155 TYR 0.010 0.001 TYR A 654 PHE 0.011 0.001 PHE A 613 TRP 0.008 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7535) covalent geometry : angle 0.51331 (10601) hydrogen bonds : bond 0.03732 ( 344) hydrogen bonds : angle 3.88505 ( 910) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.8318 (mm) cc_final: 0.8017 (pt) REVERT: A 398 THR cc_start: 0.9152 (m) cc_final: 0.8894 (t) outliers start: 5 outliers final: 5 residues processed: 80 average time/residue: 0.2955 time to fit residues: 29.0126 Evaluate side-chains 78 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 0.0040 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 48 optimal weight: 0.0270 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.4652 ------------------------------------------------------------------------------- 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 = 0.3172 r_free = 0.3172 target = 0.078609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.068937 restraints weight = 43424.625| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.65 r_work: 0.2888 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7535 Z= 0.115 Angle : 0.506 4.315 10601 Z= 0.283 Chirality : 0.037 0.133 1207 Planarity : 0.004 0.040 1048 Dihedral : 21.351 168.766 1908 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.70 % Allowed : 15.36 % Favored : 83.94 % 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: 1.01 (0.34), residues: 663 helix: 2.16 (0.31), residues: 304 sheet: -1.19 (0.58), residues: 64 loop : -0.46 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 155 TYR 0.010 0.001 TYR A 654 PHE 0.011 0.001 PHE A 613 TRP 0.009 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7535) covalent geometry : angle 0.50612 (10601) hydrogen bonds : bond 0.03621 ( 344) hydrogen bonds : angle 3.85274 ( 910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3346.54 seconds wall clock time: 57 minutes 27.72 seconds (3447.72 seconds total)