Starting phenix.real_space_refine on Wed Jun 4 22:52:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hff_34719/06_2025/8hff_34719.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hff_34719/06_2025/8hff_34719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hff_34719/06_2025/8hff_34719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hff_34719/06_2025/8hff_34719.map" model { file = "/net/cci-nas-00/data/ceres_data/8hff_34719/06_2025/8hff_34719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hff_34719/06_2025/8hff_34719.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.127 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2953 2.51 5 N 681 2.21 5 O 745 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4399 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4373 Classifications: {'peptide': 547} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Unusual residues: {'LNR': 2} Classifications: {'undetermined': 2, 'water': 2} Link IDs: {None: 3} Time building chain proxies: 3.47, per 1000 atoms: 0.79 Number of scatterers: 4399 At special positions: 0 Unit cell: (70.3625, 69.28, 98.5075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 745 8.00 N 681 7.00 C 2953 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: 1.06 Conformation dependent library (CDL) restraints added in 502.1 milliseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 82.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.649A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.468A 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 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.691A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.839A 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 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 255 through 261 removed outlier: 3.639A pdb=" N THR A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 261 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 283 removed outlier: 3.817A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 3.906A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.714A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.968A pdb=" N TYR A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 385 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.615A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.796A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 497 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: 3.587A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.507A pdb=" N ILE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 604 removed outlier: 4.040A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS A 599 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.759A 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 545 302 hydrogen bonds defined for protein. 867 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: 1.21 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 649 1.29 - 1.42: 1370 1.42 - 1.55: 2488 1.55 - 1.68: 0 1.68 - 1.81: 31 Bond restraints: 4538 Sorted by residual: bond pdb=" C GLY A 92 " pdb=" O GLY A 92 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.35e-02 5.49e+03 2.98e+01 bond pdb=" C ASN A 89 " pdb=" O ASN A 89 " ideal model delta sigma weight residual 1.232 1.167 0.065 1.36e-02 5.41e+03 2.31e+01 bond pdb=" C GLY A 92 " pdb=" N ALA A 93 " ideal model delta sigma weight residual 1.332 1.268 0.064 1.40e-02 5.10e+03 2.09e+01 bond pdb=" C GLY A 91 " pdb=" O GLY A 91 " ideal model delta sigma weight residual 1.235 1.186 0.048 1.35e-02 5.49e+03 1.28e+01 bond pdb=" C GLY A 90 " pdb=" O GLY A 90 " ideal model delta sigma weight residual 1.235 1.191 0.043 1.35e-02 5.49e+03 1.03e+01 ... (remaining 4533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 6006 1.31 - 2.61: 131 2.61 - 3.92: 40 3.92 - 5.22: 12 5.22 - 6.53: 1 Bond angle restraints: 6190 Sorted by residual: angle pdb=" CA ASN A 89 " pdb=" C ASN A 89 " pdb=" O ASN A 89 " ideal model delta sigma weight residual 121.17 117.39 3.78 1.24e+00 6.50e-01 9.29e+00 angle pdb=" N GLY A 90 " pdb=" CA GLY A 90 " pdb=" C GLY A 90 " ideal model delta sigma weight residual 113.18 119.71 -6.53 2.37e+00 1.78e-01 7.59e+00 angle pdb=" C ASN A 89 " pdb=" CA ASN A 89 " pdb=" CB ASN A 89 " ideal model delta sigma weight residual 111.23 115.90 -4.67 1.70e+00 3.46e-01 7.53e+00 angle pdb=" C PHE A 150 " pdb=" N TYR A 151 " pdb=" CA TYR A 151 " ideal model delta sigma weight residual 121.14 116.53 4.61 1.75e+00 3.27e-01 6.93e+00 angle pdb=" CA TYR A 151 " pdb=" CB TYR A 151 " pdb=" CG TYR A 151 " ideal model delta sigma weight residual 113.90 118.52 -4.62 1.80e+00 3.09e-01 6.59e+00 ... (remaining 6185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 2209 17.79 - 35.58: 251 35.58 - 53.37: 61 53.37 - 71.16: 15 71.16 - 88.95: 1 Dihedral angle restraints: 2537 sinusoidal: 957 harmonic: 1580 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 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+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 -131.34 8.74 0 2.50e+00 1.60e-01 1.22e+01 dihedral pdb=" CA ASP A 64 " pdb=" CB ASP A 64 " pdb=" CG ASP A 64 " pdb=" OD1 ASP A 64 " ideal model delta sinusoidal sigma weight residual -30.00 -89.91 59.91 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 2534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 633 0.067 - 0.135: 54 0.135 - 0.202: 3 0.202 - 0.270: 0 0.270 - 0.337: 1 Chirality restraints: 691 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 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CAL LNR A 702 " pdb=" CAH LNR A 702 " pdb=" CAK LNR A 702 " pdb=" OAD LNR A 702 " both_signs ideal model delta sigma weight residual False -2.28 -2.43 0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 688 not shown) Planarity restraints: 751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ILE A 103 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 89 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C ASN A 89 " 0.056 2.00e-02 2.50e+03 pdb=" O ASN A 89 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY A 90 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 88 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C LYS A 88 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS A 88 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 89 " 0.017 2.00e-02 2.50e+03 ... (remaining 748 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 79 2.69 - 3.25: 4446 3.25 - 3.80: 7147 3.80 - 4.35: 9270 4.35 - 4.90: 16096 Nonbonded interactions: 37038 Sorted by model distance: nonbonded pdb=" OD1 ASP A 75 " pdb=" OG SER A 419 " model vdw 2.142 3.040 nonbonded pdb=" O ALA A 328 " pdb=" OG SER A 331 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASN A 337 " pdb=" N ASN A 338 " model vdw 2.287 3.120 nonbonded pdb=" O THR A 283 " pdb=" OG1 THR A 283 " model vdw 2.327 3.040 nonbonded pdb=" N ASP A 175 " pdb=" OD1 ASP A 175 " model vdw 2.367 3.120 ... (remaining 37033 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.240 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 4539 Z= 0.217 Angle : 0.544 6.527 6192 Z= 0.292 Chirality : 0.040 0.337 691 Planarity : 0.004 0.039 751 Dihedral : 16.022 88.952 1528 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.08 % Allowed : 19.52 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.38), residues: 543 helix: 1.68 (0.28), residues: 376 sheet: None (None), residues: 0 loop : 0.60 (0.53), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.001 0.000 HIS A 296 PHE 0.009 0.001 PHE A 362 TYR 0.018 0.001 TYR A 151 ARG 0.001 0.000 ARG A 607 Details of bonding type rmsd hydrogen bonds : bond 0.12187 ( 302) hydrogen bonds : angle 5.45337 ( 867) SS BOND : bond 0.00176 ( 1) SS BOND : angle 0.56834 ( 2) covalent geometry : bond 0.00368 ( 4538) covalent geometry : angle 0.54388 ( 6190) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.461 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 57 average time/residue: 0.7523 time to fit residues: 45.8007 Evaluate side-chains 54 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 498 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.148656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113843 restraints weight = 5203.138| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.99 r_work: 0.3173 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4539 Z= 0.151 Angle : 0.532 8.089 6192 Z= 0.277 Chirality : 0.040 0.150 691 Planarity : 0.004 0.047 751 Dihedral : 5.938 58.160 607 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.17 % Allowed : 16.49 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.38), residues: 543 helix: 1.69 (0.27), residues: 382 sheet: None (None), residues: 0 loop : 0.47 (0.54), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.016 0.001 PHE A 101 TYR 0.017 0.001 TYR A 84 ARG 0.002 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.05221 ( 302) hydrogen bonds : angle 4.95815 ( 867) SS BOND : bond 0.00315 ( 1) SS BOND : angle 0.94535 ( 2) covalent geometry : bond 0.00361 ( 4538) covalent geometry : angle 0.53148 ( 6190) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.473 Fit side-chains REVERT: A 329 PHE cc_start: 0.7801 (m-80) cc_final: 0.7464 (m-10) REVERT: A 459 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6480 (t80) outliers start: 10 outliers final: 2 residues processed: 55 average time/residue: 0.6314 time to fit residues: 37.4920 Evaluate side-chains 48 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.154566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116130 restraints weight = 5133.377| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.43 r_work: 0.3162 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4539 Z= 0.182 Angle : 0.542 8.598 6192 Z= 0.286 Chirality : 0.041 0.158 691 Planarity : 0.004 0.048 751 Dihedral : 5.440 53.468 602 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.39 % Allowed : 16.70 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.37), residues: 543 helix: 1.53 (0.27), residues: 383 sheet: None (None), residues: 0 loop : 0.43 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.003 0.000 HIS A 280 PHE 0.012 0.002 PHE A 94 TYR 0.019 0.001 TYR A 84 ARG 0.002 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.05681 ( 302) hydrogen bonds : angle 5.03127 ( 867) SS BOND : bond 0.00306 ( 1) SS BOND : angle 0.92968 ( 2) covalent geometry : bond 0.00450 ( 4538) covalent geometry : angle 0.54228 ( 6190) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 329 PHE cc_start: 0.7916 (m-80) cc_final: 0.7581 (m-10) REVERT: A 365 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6519 (pt) REVERT: A 459 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.6699 (t80) outliers start: 11 outliers final: 3 residues processed: 51 average time/residue: 0.6304 time to fit residues: 34.7165 Evaluate side-chains 46 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 365 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 11 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 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 = 0.3705 r_free = 0.3705 target = 0.149434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115133 restraints weight = 5244.590| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.01 r_work: 0.3158 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4539 Z= 0.142 Angle : 0.505 7.564 6192 Z= 0.267 Chirality : 0.040 0.150 691 Planarity : 0.004 0.050 751 Dihedral : 5.073 47.393 602 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.04 % Allowed : 16.49 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.37), residues: 543 helix: 1.63 (0.27), residues: 385 sheet: None (None), residues: 0 loop : 0.46 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.012 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.002 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.04997 ( 302) hydrogen bonds : angle 4.86370 ( 867) SS BOND : bond 0.00274 ( 1) SS BOND : angle 0.83572 ( 2) covalent geometry : bond 0.00336 ( 4538) covalent geometry : angle 0.50525 ( 6190) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 329 PHE cc_start: 0.7837 (m-80) cc_final: 0.7497 (m-10) REVERT: A 459 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.6434 (t80) REVERT: A 509 MET cc_start: 0.8156 (mtm) cc_final: 0.7660 (mtm) outliers start: 14 outliers final: 5 residues processed: 55 average time/residue: 0.6248 time to fit residues: 37.0417 Evaluate side-chains 49 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN A 507 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109747 restraints weight = 5318.740| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.06 r_work: 0.3155 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4539 Z= 0.141 Angle : 0.501 7.687 6192 Z= 0.263 Chirality : 0.039 0.154 691 Planarity : 0.004 0.051 751 Dihedral : 4.939 42.174 602 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.39 % Allowed : 18.22 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.37), residues: 543 helix: 1.72 (0.27), residues: 383 sheet: None (None), residues: 0 loop : 0.47 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.011 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.04993 ( 302) hydrogen bonds : angle 4.82806 ( 867) SS BOND : bond 0.00249 ( 1) SS BOND : angle 0.75742 ( 2) covalent geometry : bond 0.00334 ( 4538) covalent geometry : angle 0.50050 ( 6190) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8335 (m110) cc_final: 0.7844 (m110) REVERT: A 329 PHE cc_start: 0.7691 (m-80) cc_final: 0.7346 (m-10) REVERT: A 371 GLU cc_start: 0.7753 (tp30) cc_final: 0.7097 (tt0) REVERT: A 459 PHE cc_start: 0.7567 (OUTLIER) cc_final: 0.6476 (t80) REVERT: A 509 MET cc_start: 0.8044 (mtm) cc_final: 0.7539 (mtm) outliers start: 11 outliers final: 5 residues processed: 53 average time/residue: 0.7242 time to fit residues: 41.1018 Evaluate side-chains 48 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 chunk 53 optimal weight: 0.0170 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.153143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119280 restraints weight = 5216.112| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.01 r_work: 0.3222 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4539 Z= 0.116 Angle : 0.473 6.413 6192 Z= 0.249 Chirality : 0.038 0.144 691 Planarity : 0.004 0.052 751 Dihedral : 4.600 36.728 602 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.60 % Allowed : 18.87 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.37), residues: 543 helix: 1.87 (0.27), residues: 383 sheet: None (None), residues: 0 loop : 0.48 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.001 0.000 HIS A 280 PHE 0.011 0.001 PHE A 110 TYR 0.014 0.001 TYR A 84 ARG 0.001 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 302) hydrogen bonds : angle 4.66569 ( 867) SS BOND : bond 0.00220 ( 1) SS BOND : angle 0.64119 ( 2) covalent geometry : bond 0.00258 ( 4538) covalent geometry : angle 0.47275 ( 6190) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8328 (m110) cc_final: 0.8079 (m110) REVERT: A 329 PHE cc_start: 0.7769 (m-80) cc_final: 0.7438 (m-10) REVERT: A 371 GLU cc_start: 0.7780 (tp30) cc_final: 0.7147 (tt0) REVERT: A 459 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.6387 (t80) REVERT: A 509 MET cc_start: 0.8161 (mtm) cc_final: 0.7762 (mtm) outliers start: 12 outliers final: 5 residues processed: 59 average time/residue: 0.6790 time to fit residues: 43.1041 Evaluate side-chains 50 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.152220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118808 restraints weight = 5207.333| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.98 r_work: 0.3215 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4539 Z= 0.123 Angle : 0.481 6.979 6192 Z= 0.253 Chirality : 0.039 0.149 691 Planarity : 0.004 0.052 751 Dihedral : 4.390 31.465 600 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.52 % Allowed : 21.04 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.37), residues: 543 helix: 1.89 (0.27), residues: 384 sheet: None (None), residues: 0 loop : 0.40 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.002 0.000 HIS A 280 PHE 0.011 0.001 PHE A 110 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 302) hydrogen bonds : angle 4.65576 ( 867) SS BOND : bond 0.00321 ( 1) SS BOND : angle 0.74673 ( 2) covalent geometry : bond 0.00280 ( 4538) covalent geometry : angle 0.48041 ( 6190) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.777 Fit side-chains REVERT: A 78 ASN cc_start: 0.8340 (m110) cc_final: 0.8085 (m110) REVERT: A 329 PHE cc_start: 0.7812 (m-80) cc_final: 0.7500 (m-10) REVERT: A 371 GLU cc_start: 0.7786 (tp30) cc_final: 0.7178 (tt0) REVERT: A 459 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.6474 (t80) REVERT: A 509 MET cc_start: 0.8160 (mtm) cc_final: 0.7787 (mtm) outliers start: 7 outliers final: 4 residues processed: 51 average time/residue: 0.8097 time to fit residues: 44.5000 Evaluate side-chains 48 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.147043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112746 restraints weight = 5276.264| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.03 r_work: 0.3152 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4539 Z= 0.150 Angle : 0.507 8.135 6192 Z= 0.266 Chirality : 0.040 0.158 691 Planarity : 0.004 0.053 751 Dihedral : 4.576 33.800 600 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.17 % Allowed : 20.39 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.37), residues: 543 helix: 1.73 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.40 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 235 HIS 0.002 0.000 HIS A 280 PHE 0.018 0.001 PHE A 164 TYR 0.018 0.001 TYR A 84 ARG 0.001 0.000 ARG A 607 Details of bonding type rmsd hydrogen bonds : bond 0.05090 ( 302) hydrogen bonds : angle 4.80380 ( 867) SS BOND : bond 0.00372 ( 1) SS BOND : angle 0.92672 ( 2) covalent geometry : bond 0.00358 ( 4538) covalent geometry : angle 0.50632 ( 6190) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.476 Fit side-chains REVERT: A 78 ASN cc_start: 0.8320 (m110) cc_final: 0.7812 (m110) REVERT: A 329 PHE cc_start: 0.7780 (m-80) cc_final: 0.7449 (m-10) REVERT: A 371 GLU cc_start: 0.7791 (tp30) cc_final: 0.7167 (tt0) REVERT: A 459 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.6635 (t80) REVERT: A 509 MET cc_start: 0.8100 (mtm) cc_final: 0.7703 (mtm) outliers start: 10 outliers final: 4 residues processed: 51 average time/residue: 0.6566 time to fit residues: 36.1182 Evaluate side-chains 47 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 437 VAL 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 51 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109547 restraints weight = 5333.713| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.06 r_work: 0.3154 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4539 Z= 0.146 Angle : 0.502 7.632 6192 Z= 0.264 Chirality : 0.040 0.155 691 Planarity : 0.004 0.053 751 Dihedral : 4.545 33.397 600 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.87 % Allowed : 21.69 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.37), residues: 543 helix: 1.74 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.35 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 235 HIS 0.002 0.000 HIS A 280 PHE 0.011 0.001 PHE A 110 TYR 0.018 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.05013 ( 302) hydrogen bonds : angle 4.80020 ( 867) SS BOND : bond 0.00401 ( 1) SS BOND : angle 0.94499 ( 2) covalent geometry : bond 0.00347 ( 4538) covalent geometry : angle 0.50167 ( 6190) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.897 Fit side-chains REVERT: A 78 ASN cc_start: 0.8275 (m110) cc_final: 0.7758 (m110) REVERT: A 329 PHE cc_start: 0.7706 (m-80) cc_final: 0.7388 (m-10) REVERT: A 371 GLU cc_start: 0.7747 (tp30) cc_final: 0.7121 (tt0) REVERT: A 459 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.6687 (t80) REVERT: A 509 MET cc_start: 0.8023 (mtm) cc_final: 0.7634 (mtm) outliers start: 4 outliers final: 2 residues processed: 45 average time/residue: 1.1580 time to fit residues: 56.0794 Evaluate side-chains 44 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.148569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114407 restraints weight = 5242.489| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.04 r_work: 0.3179 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4539 Z= 0.132 Angle : 0.488 7.060 6192 Z= 0.257 Chirality : 0.039 0.150 691 Planarity : 0.004 0.052 751 Dihedral : 4.449 32.276 600 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.87 % Allowed : 21.69 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.37), residues: 543 helix: 1.77 (0.27), residues: 385 sheet: None (None), residues: 0 loop : 0.38 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.019 0.001 PHE A 164 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04770 ( 302) hydrogen bonds : angle 4.73413 ( 867) SS BOND : bond 0.00356 ( 1) SS BOND : angle 0.90177 ( 2) covalent geometry : bond 0.00308 ( 4538) covalent geometry : angle 0.48820 ( 6190) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 1.105 Fit side-chains REVERT: A 78 ASN cc_start: 0.8295 (m110) cc_final: 0.7950 (m110) REVERT: A 329 PHE cc_start: 0.7769 (m-80) cc_final: 0.7469 (m-10) REVERT: A 371 GLU cc_start: 0.7763 (tp30) cc_final: 0.7153 (tt0) REVERT: A 459 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.6610 (t80) outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 1.2748 time to fit residues: 65.7092 Evaluate side-chains 47 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 0.0270 chunk 36 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.153619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119824 restraints weight = 5252.264| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.05 r_work: 0.3248 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4539 Z= 0.109 Angle : 0.459 5.764 6192 Z= 0.243 Chirality : 0.038 0.139 691 Planarity : 0.004 0.051 751 Dihedral : 4.194 29.643 600 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.30 % Allowed : 21.48 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.37), residues: 543 helix: 1.92 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.36 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 553 HIS 0.001 0.000 HIS A 613 PHE 0.011 0.001 PHE A 110 TYR 0.013 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 302) hydrogen bonds : angle 4.52653 ( 867) SS BOND : bond 0.00288 ( 1) SS BOND : angle 0.74505 ( 2) covalent geometry : bond 0.00235 ( 4538) covalent geometry : angle 0.45862 ( 6190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3449.43 seconds wall clock time: 61 minutes 51.18 seconds (3711.18 seconds total)