Starting phenix.real_space_refine on Sat Jun 7 12:58:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3v_35157/06_2025/8i3v_35157_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3v_35157/06_2025/8i3v_35157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i3v_35157/06_2025/8i3v_35157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3v_35157/06_2025/8i3v_35157.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3v_35157/06_2025/8i3v_35157_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3v_35157/06_2025/8i3v_35157_trim.cif" } resolution = 2.85 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= 0.003 sd= 0.135 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: 7 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 C 2965 2.51 5 N 681 2.21 5 O 751 1.98 5 F 1 1.80 5 H 4373 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 8792 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8756 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 528} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 36 Unusual residues: {' CL': 1, '68P': 1} Classifications: {'undetermined': 2, 'water': 11} Link IDs: {None: 12} Time building chain proxies: 4.61, per 1000 atoms: 0.52 Number of scatterers: 8792 At special positions: 0 Unit cell: (70.3625, 70.3625, 98.5075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 20 16.00 F 1 9.00 O 751 8.00 N 681 7.00 C 2965 6.00 H 4373 1.00 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: 2.62 Conformation dependent library (CDL) restraints added in 770.9 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1008 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 1 sheets defined 81.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 60 through 73 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.569A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.560A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.610A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 262 through 283 removed outlier: 3.986A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 3.862A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.575A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.727A pdb=" N GLU A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.734A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) 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: 3.576A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.604A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 496 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.610A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 592 Processing helix chain 'A' and resid 594 through 601 removed outlier: 3.812A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.376A 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 616 removed outlier: 3.808A 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 545 295 hydrogen bonds defined for protein. 849 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: 3.42 Time building geometry restraints manager: 3.09 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: 4366 1.03 - 1.23: 13 1.23 - 1.42: 2017 1.42 - 1.62: 2497 1.62 - 1.81: 31 Bond restraints: 8924 Sorted by residual: bond pdb=" N GLY A 60 " pdb=" CA GLY A 60 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.20e+00 bond pdb=" N GLY A 60 " pdb=" H GLY A 60 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" CA LEU A 102 " pdb=" C LEU A 102 " ideal model delta sigma weight residual 1.524 1.509 0.016 1.28e-02 6.10e+03 1.48e+00 bond pdb=" C23 68P A 701 " pdb=" N03 68P A 701 " ideal model delta sigma weight residual 1.447 1.467 -0.020 2.00e-02 2.50e+03 9.68e-01 bond pdb=" C05 68P A 701 " pdb=" O02 68P A 701 " ideal model delta sigma weight residual 1.420 1.440 -0.020 2.00e-02 2.50e+03 9.59e-01 ... (remaining 8919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.28: 16077 7.28 - 14.56: 0 14.56 - 21.84: 0 21.84 - 29.12: 0 29.12 - 36.40: 3 Bond angle restraints: 16080 Sorted by residual: angle pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 109.00 72.60 36.40 3.00e+00 1.11e-01 1.47e+02 angle pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 110.00 76.44 33.56 3.00e+00 1.11e-01 1.25e+02 angle pdb=" CB TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 109.00 77.56 31.44 3.00e+00 1.11e-01 1.10e+02 angle pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" C TYR A 205 " ideal model delta sigma weight residual 110.80 117.86 -7.06 2.13e+00 2.20e-01 1.10e+01 angle pdb=" N LEU A 102 " pdb=" CA LEU A 102 " pdb=" C LEU A 102 " ideal model delta sigma weight residual 111.02 108.23 2.79 1.22e+00 6.72e-01 5.21e+00 ... (remaining 16075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 3735 17.26 - 34.52: 337 34.52 - 51.79: 122 51.79 - 69.05: 42 69.05 - 86.31: 3 Dihedral angle restraints: 4239 sinusoidal: 2156 harmonic: 2083 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 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -132.20 9.60 0 2.50e+00 1.60e-01 1.47e+01 dihedral pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual 122.80 131.67 -8.87 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 4236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 664 0.082 - 0.164: 26 0.164 - 0.245: 0 0.245 - 0.327: 0 0.327 - 0.409: 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 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA ILE A 103 " pdb=" N ILE A 103 " pdb=" C ILE A 103 " pdb=" CB ILE A 103 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" C PRO A 132 " pdb=" CB PRO A 132 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 688 not shown) Planarity restraints: 1279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C ILE A 103 " -0.063 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 492 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C VAL A 492 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL A 492 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A 493 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 102 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C LEU A 102 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU A 102 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE A 103 " 0.011 2.00e-02 2.50e+03 ... (remaining 1276 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 857 2.24 - 2.83: 19092 2.83 - 3.42: 23948 3.42 - 4.01: 32553 4.01 - 4.60: 50443 Nonbonded interactions: 126893 Sorted by model distance: nonbonded pdb="HE21 GLN A 234 " pdb=" OE1 GLN A 236 " model vdw 1.646 2.450 nonbonded pdb=" HA TYR A 205 " pdb=" HB3 TYR A 205 " model vdw 1.665 1.952 nonbonded pdb=" HH TYR A 496 " pdb=" OD2 ASP A 504 " model vdw 1.665 2.450 nonbonded pdb="HH22 ARG A 121 " pdb=" O ASN A 333 " model vdw 1.673 2.450 nonbonded pdb=" HH TYR A 162 " pdb=" O HOH A 803 " model vdw 1.699 2.450 ... (remaining 126888 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: 0.460 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: 0.140 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.170 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 0.040 4552 Z= 0.140 Angle : 0.538 7.058 6212 Z= 0.285 Chirality : 0.039 0.409 691 Planarity : 0.004 0.037 752 Dihedral : 16.333 86.310 1542 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.61 % Rotamer: Outliers : 2.16 % Allowed : 20.78 % Favored : 77.06 % 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: 1.90 (0.38), residues: 544 helix: 1.66 (0.28), residues: 376 sheet: None (None), residues: 0 loop : 0.54 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 235 HIS 0.002 0.001 HIS A 228 PHE 0.017 0.001 PHE A 408 TYR 0.014 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.11898 ( 295) hydrogen bonds : angle 5.07827 ( 849) SS BOND : bond 0.00303 ( 1) SS BOND : angle 0.72179 ( 2) covalent geometry : bond 0.00295 ( 4551) covalent geometry : angle 0.53766 ( 6210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.609 Fit side-chains REVERT: A 100 LEU cc_start: 0.8089 (tp) cc_final: 0.7884 (tp) outliers start: 10 outliers final: 7 residues processed: 51 average time/residue: 1.2003 time to fit residues: 66.4676 Evaluate side-chains 49 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 399 SER 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: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.123323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.101710 restraints weight = 15501.684| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.71 r_work: 0.3085 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4552 Z= 0.190 Angle : 0.554 7.336 6212 Z= 0.291 Chirality : 0.042 0.418 691 Planarity : 0.004 0.037 752 Dihedral : 5.594 55.586 621 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.61 % Rotamer: Outliers : 2.38 % Allowed : 18.83 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.55 (0.37), residues: 544 helix: 1.43 (0.27), residues: 383 sheet: None (None), residues: 0 loop : 0.24 (0.53), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 128 HIS 0.003 0.001 HIS A 441 PHE 0.016 0.002 PHE A 408 TYR 0.017 0.001 TYR A 84 ARG 0.002 0.000 ARG A 442 Details of bonding type rmsd hydrogen bonds : bond 0.05404 ( 295) hydrogen bonds : angle 4.71387 ( 849) SS BOND : bond 0.00349 ( 1) SS BOND : angle 1.00095 ( 2) covalent geometry : bond 0.00457 ( 4551) covalent geometry : angle 0.55331 ( 6210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.799 Fit side-chains REVERT: A 152 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.7402 (t80) REVERT: A 431 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7215 (mm) REVERT: A 603 GLN cc_start: 0.7817 (mt0) cc_final: 0.6966 (mm110) outliers start: 11 outliers final: 4 residues processed: 57 average time/residue: 1.5542 time to fit residues: 95.7519 Evaluate side-chains 52 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 431 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.101984 restraints weight = 15543.745| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.72 r_work: 0.3062 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4552 Z= 0.150 Angle : 0.516 6.951 6212 Z= 0.270 Chirality : 0.040 0.414 691 Planarity : 0.004 0.037 752 Dihedral : 5.395 57.426 616 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 2.16 % Allowed : 18.61 % Favored : 79.22 % 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: 1.71 (0.37), residues: 544 helix: 1.63 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.10 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 235 HIS 0.002 0.001 HIS A 599 PHE 0.014 0.001 PHE A 408 TYR 0.015 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04991 ( 295) hydrogen bonds : angle 4.54874 ( 849) SS BOND : bond 0.00256 ( 1) SS BOND : angle 0.77995 ( 2) covalent geometry : bond 0.00354 ( 4551) covalent geometry : angle 0.51579 ( 6210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.663 Fit side-chains REVERT: A 152 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.7461 (t80) REVERT: A 431 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7288 (mm) REVERT: A 603 GLN cc_start: 0.7838 (mt0) cc_final: 0.7014 (mm110) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 1.2071 time to fit residues: 68.6113 Evaluate side-chains 49 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 600 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.102631 restraints weight = 15286.379| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.70 r_work: 0.3098 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4552 Z= 0.138 Angle : 0.501 6.958 6212 Z= 0.263 Chirality : 0.040 0.412 691 Planarity : 0.004 0.038 752 Dihedral : 4.590 19.211 614 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.02 % Favored : 97.79 % Rotamer: Outliers : 1.95 % Allowed : 19.05 % Favored : 79.00 % 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: 1.82 (0.37), residues: 544 helix: 1.77 (0.27), residues: 374 sheet: None (None), residues: 0 loop : 0.04 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.003 0.001 HIS A 599 PHE 0.011 0.001 PHE A 362 TYR 0.014 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 295) hydrogen bonds : angle 4.50344 ( 849) SS BOND : bond 0.00250 ( 1) SS BOND : angle 0.72239 ( 2) covalent geometry : bond 0.00325 ( 4551) covalent geometry : angle 0.50056 ( 6210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.686 Fit side-chains REVERT: A 152 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.7387 (t80) REVERT: A 431 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7061 (mm) REVERT: A 603 GLN cc_start: 0.7824 (mt0) cc_final: 0.6975 (mm110) outliers start: 9 outliers final: 4 residues processed: 49 average time/residue: 1.3285 time to fit residues: 70.9541 Evaluate side-chains 47 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 600 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.122630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.101276 restraints weight = 15492.839| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.70 r_work: 0.3051 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4552 Z= 0.155 Angle : 0.514 6.949 6212 Z= 0.270 Chirality : 0.040 0.415 691 Planarity : 0.004 0.038 752 Dihedral : 4.786 23.022 613 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 2.16 % Allowed : 18.18 % Favored : 79.65 % 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: 1.76 (0.37), residues: 544 helix: 1.72 (0.27), residues: 374 sheet: None (None), residues: 0 loop : 0.01 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.002 0.001 HIS A 613 PHE 0.013 0.001 PHE A 362 TYR 0.016 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04986 ( 295) hydrogen bonds : angle 4.55099 ( 849) SS BOND : bond 0.00264 ( 1) SS BOND : angle 0.65922 ( 2) covalent geometry : bond 0.00372 ( 4551) covalent geometry : angle 0.51401 ( 6210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.700 Fit side-chains REVERT: A 152 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.7510 (t80) REVERT: A 603 GLN cc_start: 0.7892 (mt0) cc_final: 0.7023 (mm110) outliers start: 10 outliers final: 3 residues processed: 54 average time/residue: 1.0325 time to fit residues: 61.5180 Evaluate side-chains 47 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 377 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.122854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.101674 restraints weight = 15455.700| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.69 r_work: 0.3052 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4552 Z= 0.147 Angle : 0.502 6.838 6212 Z= 0.264 Chirality : 0.040 0.414 691 Planarity : 0.004 0.038 752 Dihedral : 4.625 20.489 613 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 1.52 % Allowed : 19.26 % Favored : 79.22 % 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: 1.81 (0.37), residues: 544 helix: 1.76 (0.27), residues: 374 sheet: None (None), residues: 0 loop : 0.04 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 PHE 0.012 0.001 PHE A 362 TYR 0.015 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04858 ( 295) hydrogen bonds : angle 4.51604 ( 849) SS BOND : bond 0.00266 ( 1) SS BOND : angle 0.70190 ( 2) covalent geometry : bond 0.00348 ( 4551) covalent geometry : angle 0.50176 ( 6210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.630 Fit side-chains REVERT: A 152 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.7526 (t80) REVERT: A 603 GLN cc_start: 0.7882 (mt0) cc_final: 0.7035 (mm110) outliers start: 7 outliers final: 2 residues processed: 50 average time/residue: 1.0030 time to fit residues: 55.2493 Evaluate side-chains 46 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 377 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.101367 restraints weight = 15601.872| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.70 r_work: 0.3051 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4552 Z= 0.149 Angle : 0.506 6.775 6212 Z= 0.266 Chirality : 0.040 0.414 691 Planarity : 0.004 0.038 752 Dihedral : 4.674 21.175 613 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 1.52 % Allowed : 19.48 % Favored : 79.00 % 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: 1.78 (0.37), residues: 544 helix: 1.77 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -0.04 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 PHE 0.012 0.001 PHE A 362 TYR 0.015 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 295) hydrogen bonds : angle 4.51534 ( 849) SS BOND : bond 0.00278 ( 1) SS BOND : angle 0.69969 ( 2) covalent geometry : bond 0.00354 ( 4551) covalent geometry : angle 0.50579 ( 6210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.729 Fit side-chains REVERT: A 152 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.7537 (t80) REVERT: A 603 GLN cc_start: 0.7888 (mt0) cc_final: 0.7051 (mm110) outliers start: 7 outliers final: 2 residues processed: 52 average time/residue: 0.9985 time to fit residues: 57.4057 Evaluate side-chains 47 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 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 = 0.3397 r_free = 0.3397 target = 0.124113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.103012 restraints weight = 15413.885| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.69 r_work: 0.3074 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4552 Z= 0.121 Angle : 0.485 6.644 6212 Z= 0.253 Chirality : 0.039 0.412 691 Planarity : 0.004 0.037 752 Dihedral : 4.377 17.112 613 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 1.95 % Allowed : 19.26 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.91 (0.37), residues: 544 helix: 1.85 (0.27), residues: 374 sheet: None (None), residues: 0 loop : 0.04 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 235 HIS 0.002 0.001 HIS A 599 PHE 0.011 0.001 PHE A 362 TYR 0.013 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 295) hydrogen bonds : angle 4.42111 ( 849) SS BOND : bond 0.00234 ( 1) SS BOND : angle 0.63745 ( 2) covalent geometry : bond 0.00280 ( 4551) covalent geometry : angle 0.48473 ( 6210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.635 Fit side-chains REVERT: A 152 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7460 (t80) REVERT: A 341 ARG cc_start: 0.7231 (ttm170) cc_final: 0.6959 (tmm160) REVERT: A 603 GLN cc_start: 0.7891 (mt0) cc_final: 0.7056 (mm110) outliers start: 9 outliers final: 4 residues processed: 53 average time/residue: 1.2791 time to fit residues: 73.6176 Evaluate side-chains 49 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 256 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 6 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 52 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 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 = 0.3404 r_free = 0.3404 target = 0.124658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103605 restraints weight = 15481.682| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.69 r_work: 0.3078 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4552 Z= 0.115 Angle : 0.483 6.609 6212 Z= 0.251 Chirality : 0.039 0.411 691 Planarity : 0.004 0.037 752 Dihedral : 4.282 16.351 613 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 1.52 % Allowed : 20.35 % Favored : 78.14 % 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: 544 helix: 1.91 (0.27), residues: 373 sheet: None (None), residues: 0 loop : 0.05 (0.52), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 PHE 0.010 0.001 PHE A 362 TYR 0.013 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 295) hydrogen bonds : angle 4.39218 ( 849) SS BOND : bond 0.00211 ( 1) SS BOND : angle 0.62353 ( 2) covalent geometry : bond 0.00263 ( 4551) covalent geometry : angle 0.48340 ( 6210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.684 Fit side-chains REVERT: A 152 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.7422 (t80) REVERT: A 341 ARG cc_start: 0.7202 (ttm170) cc_final: 0.6921 (tmm160) REVERT: A 603 GLN cc_start: 0.7852 (mt0) cc_final: 0.7051 (mm110) outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 1.6330 time to fit residues: 89.1084 Evaluate side-chains 49 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 256 VAL 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 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.125703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.104597 restraints weight = 15233.321| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.69 r_work: 0.3093 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4552 Z= 0.107 Angle : 0.473 6.563 6212 Z= 0.245 Chirality : 0.039 0.411 691 Planarity : 0.004 0.036 752 Dihedral : 4.126 14.976 613 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.02 % Favored : 97.79 % Rotamer: Outliers : 1.08 % Allowed : 20.78 % Favored : 78.14 % 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 (0.38), residues: 544 helix: 1.91 (0.27), residues: 376 sheet: None (None), residues: 0 loop : 0.11 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 PHE 0.009 0.001 PHE A 362 TYR 0.012 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 295) hydrogen bonds : angle 4.33394 ( 849) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.56199 ( 2) covalent geometry : bond 0.00242 ( 4551) covalent geometry : angle 0.47336 ( 6210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.683 Fit side-chains REVERT: A 75 ASP cc_start: 0.7966 (t0) cc_final: 0.7702 (t0) REVERT: A 152 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7305 (t80) REVERT: A 341 ARG cc_start: 0.7236 (ttm170) cc_final: 0.6913 (tmm160) REVERT: A 374 VAL cc_start: 0.8556 (m) cc_final: 0.8328 (p) REVERT: A 603 GLN cc_start: 0.7845 (mt0) cc_final: 0.7047 (mm110) outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 1.3162 time to fit residues: 73.8618 Evaluate side-chains 48 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 256 VAL 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 31 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.126019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.104921 restraints weight = 15299.632| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.70 r_work: 0.3097 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4552 Z= 0.109 Angle : 0.485 6.560 6212 Z= 0.249 Chirality : 0.039 0.411 691 Planarity : 0.004 0.036 752 Dihedral : 4.104 14.532 613 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 1.08 % Allowed : 20.78 % Favored : 78.14 % 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: 2.04 (0.37), residues: 544 helix: 1.94 (0.27), residues: 376 sheet: None (None), residues: 0 loop : 0.10 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 PHE 0.009 0.001 PHE A 362 TYR 0.012 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 295) hydrogen bonds : angle 4.31034 ( 849) SS BOND : bond 0.00147 ( 1) SS BOND : angle 0.50718 ( 2) covalent geometry : bond 0.00249 ( 4551) covalent geometry : angle 0.48512 ( 6210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5751.83 seconds wall clock time: 101 minutes 54.05 seconds (6114.05 seconds total)