Starting phenix.real_space_refine on Fri May 9 20:15:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw9_39626/05_2025/8yw9_39626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw9_39626/05_2025/8yw9_39626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yw9_39626/05_2025/8yw9_39626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw9_39626/05_2025/8yw9_39626.map" model { file = "/net/cci-nas-00/data/ceres_data/8yw9_39626/05_2025/8yw9_39626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw9_39626/05_2025/8yw9_39626.cif" } resolution = 3.01 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= 0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 21 5.16 5 C 2391 2.51 5 N 630 2.21 5 O 665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3709 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 984 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Chain: "A" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 754 Classifications: {'peptide': 94} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 89} Chain: "C" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1003 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "D" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 879 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 89 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 3.18, per 1000 atoms: 0.86 Number of scatterers: 3709 At special positions: 0 Unit cell: (82.08, 98.04, 96.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 2 15.00 O 665 8.00 N 630 7.00 C 2391 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 400.6 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 832 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 7 sheets defined 46.3% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 40 through 48 removed outlier: 3.718A pdb=" N TRP B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 49 through 59 Processing helix chain 'B' and resid 60 through 62 No H-bonds generated for 'chain 'B' and resid 60 through 62' Processing helix chain 'B' and resid 68 through 89 removed outlier: 3.974A pdb=" N LEU B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 126 Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 24 through 34 Proline residue: A 30 - end of helix removed outlier: 3.595A pdb=" N TRP A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 removed outlier: 3.588A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 77 through 108 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.632A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.229A pdb=" N GLY C 10 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER C 126 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL C 12 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE C 34 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.229A pdb=" N GLY C 10 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER C 126 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL C 12 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 102 through 104 Processing sheet with id=AA5, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.404A pdb=" N GLY D 10 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER D 114 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL D 12 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.404A pdb=" N GLY D 10 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER D 114 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL D 12 " --> pdb=" O SER D 114 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 582 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: 1.03 Time building geometry restraints manager: 1.05 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: 563 1.29 - 1.42: 1082 1.42 - 1.55: 2099 1.55 - 1.68: 25 1.68 - 1.80: 36 Bond restraints: 3805 Sorted by residual: bond pdb=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 1.334 1.432 -0.098 1.10e-02 8.26e+03 7.89e+01 bond pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 1.334 1.423 -0.089 1.10e-02 8.26e+03 6.49e+01 bond pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 1.342 1.444 -0.102 1.50e-02 4.44e+03 4.62e+01 bond pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 1.342 1.435 -0.093 1.50e-02 4.44e+03 3.84e+01 bond pdb=" OB2 CDL B 201 " pdb=" PB2 CDL B 201 " ideal model delta sigma weight residual 1.579 1.667 -0.088 1.50e-02 4.44e+03 3.44e+01 ... (remaining 3800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 4977 2.43 - 4.85: 140 4.85 - 7.28: 8 7.28 - 9.70: 8 9.70 - 12.13: 1 Bond angle restraints: 5134 Sorted by residual: angle pdb=" C31 CDL B 201 " pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 111.64 123.77 -12.13 1.65e+00 3.69e-01 5.43e+01 angle pdb=" C11 CDL B 201 " pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 111.33 120.84 -9.51 1.32e+00 5.72e-01 5.18e+01 angle pdb=" C51 CDL B 201 " pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 111.33 119.89 -8.56 1.32e+00 5.72e-01 4.20e+01 angle pdb=" C71 CDL B 201 " pdb=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 111.64 120.69 -9.05 1.65e+00 3.69e-01 3.03e+01 angle pdb=" C31 CDL B 201 " pdb=" CA7 CDL B 201 " pdb=" OA9 CDL B 201 " ideal model delta sigma weight residual 125.25 117.09 8.16 1.98e+00 2.56e-01 1.70e+01 ... (remaining 5129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.26: 2135 31.26 - 62.52: 107 62.52 - 93.79: 7 93.79 - 125.05: 0 125.05 - 156.31: 1 Dihedral angle restraints: 2250 sinusoidal: 935 harmonic: 1315 Sorted by residual: dihedral pdb=" CA5 CDL B 201 " pdb=" CA4 CDL B 201 " pdb=" OA6 CDL B 201 " pdb=" CA6 CDL B 201 " ideal model delta sinusoidal sigma weight residual 168.24 -35.45 -156.31 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C ASP D 52 " pdb=" N ASP D 52 " pdb=" CA ASP D 52 " pdb=" CB ASP D 52 " ideal model delta harmonic sigma weight residual -122.60 -131.96 9.36 0 2.50e+00 1.60e-01 1.40e+01 dihedral pdb=" CA TYR C 32 " pdb=" C TYR C 32 " pdb=" N ALA C 33 " pdb=" CA ALA C 33 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 2247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 426 0.058 - 0.116: 69 0.116 - 0.175: 23 0.175 - 0.233: 8 0.233 - 0.291: 1 Chirality restraints: 527 Sorted by residual: chirality pdb=" CA ASP D 52 " pdb=" N ASP D 52 " pdb=" C ASP D 52 " pdb=" CB ASP D 52 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA GLU C 105 " pdb=" N GLU C 105 " pdb=" C GLU C 105 " pdb=" CB GLU C 105 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA GLN D 54 " pdb=" N GLN D 54 " pdb=" C GLN D 54 " pdb=" CB GLN D 54 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 524 not shown) Planarity restraints: 640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 51 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C ILE C 51 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE C 51 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG C 52 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 45 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO B 46 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 46 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 46 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 103 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C TYR C 103 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR C 103 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR C 104 " 0.009 2.00e-02 2.50e+03 ... (remaining 637 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1044 2.81 - 3.33: 3163 3.33 - 3.86: 6199 3.86 - 4.38: 7509 4.38 - 4.90: 12546 Nonbonded interactions: 30461 Sorted by model distance: nonbonded pdb=" O SER A 108 " pdb=" OG SER A 108 " model vdw 2.292 3.040 nonbonded pdb=" OD1 ASP C 73 " pdb=" OG SER C 75 " model vdw 2.365 3.040 nonbonded pdb=" OE2 GLU C 6 " pdb=" N CYS C 96 " model vdw 2.386 3.120 nonbonded pdb=" OB6 CDL B 201 " pdb=" OB8 CDL B 201 " model vdw 2.408 2.432 nonbonded pdb=" O LYS A 100 " pdb=" OG1 THR A 104 " model vdw 2.430 3.040 ... (remaining 30456 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 : 0.010 0.102 3807 Z= 0.590 Angle : 0.946 12.129 5138 Z= 0.623 Chirality : 0.056 0.291 527 Planarity : 0.004 0.040 640 Dihedral : 16.927 156.308 1412 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.81 % Allowed : 12.67 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.99 (0.37), residues: 450 helix: -0.25 (0.37), residues: 170 sheet: -0.75 (0.42), residues: 130 loop : -0.73 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.005 0.001 HIS C 31 PHE 0.011 0.002 PHE A 81 TYR 0.014 0.001 TYR A 62 ARG 0.002 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.13872 ( 210) hydrogen bonds : angle 6.56224 ( 582) SS BOND : bond 0.00462 ( 2) SS BOND : angle 3.20884 ( 4) covalent geometry : bond 0.00972 ( 3805) covalent geometry : angle 0.94199 ( 5134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: B 86 SER cc_start: 0.9141 (p) cc_final: 0.8841 (m) REVERT: C 31 HIS cc_start: 0.5083 (m-70) cc_final: 0.4834 (m-70) outliers start: 3 outliers final: 0 residues processed: 40 average time/residue: 0.2056 time to fit residues: 10.1264 Evaluate side-chains 33 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 94 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.194668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.112528 restraints weight = 3700.053| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.46 r_work: 0.2984 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3807 Z= 0.154 Angle : 0.481 5.512 5138 Z= 0.259 Chirality : 0.040 0.126 527 Planarity : 0.004 0.030 640 Dihedral : 12.798 147.046 594 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.70 % Allowed : 13.21 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.49 (0.39), residues: 450 helix: 1.22 (0.40), residues: 171 sheet: -0.26 (0.40), residues: 133 loop : 0.07 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 28 HIS 0.006 0.001 HIS C 31 PHE 0.008 0.001 PHE A 69 TYR 0.017 0.001 TYR C 98 ARG 0.002 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 210) hydrogen bonds : angle 4.83168 ( 582) SS BOND : bond 0.00141 ( 2) SS BOND : angle 0.74344 ( 4) covalent geometry : bond 0.00358 ( 3805) covalent geometry : angle 0.48034 ( 5134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8498 (m-40) cc_final: 0.8138 (m110) REVERT: B 86 SER cc_start: 0.9256 (p) cc_final: 0.8915 (m) outliers start: 10 outliers final: 6 residues processed: 39 average time/residue: 0.1501 time to fit residues: 7.5986 Evaluate side-chains 36 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.188605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.104847 restraints weight = 3748.426| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.49 r_work: 0.2905 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 3807 Z= 0.305 Angle : 0.557 6.032 5138 Z= 0.298 Chirality : 0.045 0.142 527 Planarity : 0.004 0.034 640 Dihedral : 12.810 145.463 594 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.23 % Allowed : 12.94 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.40 (0.39), residues: 450 helix: 1.09 (0.39), residues: 172 sheet: -0.17 (0.43), residues: 120 loop : -0.11 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 110 HIS 0.006 0.002 HIS C 31 PHE 0.011 0.002 PHE A 69 TYR 0.014 0.002 TYR C 98 ARG 0.002 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 210) hydrogen bonds : angle 4.98709 ( 582) SS BOND : bond 0.00120 ( 2) SS BOND : angle 1.16293 ( 4) covalent geometry : bond 0.00737 ( 3805) covalent geometry : angle 0.55589 ( 5134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8691 (m-40) cc_final: 0.8436 (m110) outliers start: 12 outliers final: 10 residues processed: 40 average time/residue: 0.1379 time to fit residues: 7.3241 Evaluate side-chains 42 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.193260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.108863 restraints weight = 3689.507| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.55 r_work: 0.2965 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3807 Z= 0.143 Angle : 0.446 5.550 5138 Z= 0.240 Chirality : 0.040 0.121 527 Planarity : 0.004 0.028 640 Dihedral : 11.956 147.355 594 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.89 % Allowed : 13.48 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.00 (0.40), residues: 450 helix: 1.66 (0.40), residues: 172 sheet: 0.07 (0.44), residues: 120 loop : 0.20 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 110 HIS 0.003 0.001 HIS A 84 PHE 0.008 0.001 PHE B 43 TYR 0.012 0.001 TYR A 62 ARG 0.001 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 210) hydrogen bonds : angle 4.41496 ( 582) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.66016 ( 4) covalent geometry : bond 0.00335 ( 3805) covalent geometry : angle 0.44613 ( 5134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8673 (m-40) cc_final: 0.8448 (m110) REVERT: B 86 SER cc_start: 0.9271 (p) cc_final: 0.8926 (m) outliers start: 7 outliers final: 4 residues processed: 35 average time/residue: 0.1532 time to fit residues: 7.1233 Evaluate side-chains 34 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 112 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.193040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.108229 restraints weight = 3793.528| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.56 r_work: 0.2953 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3807 Z= 0.159 Angle : 0.447 5.631 5138 Z= 0.240 Chirality : 0.040 0.123 527 Planarity : 0.003 0.030 640 Dihedral : 11.829 147.439 594 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.89 % Allowed : 14.29 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.27 (0.40), residues: 450 helix: 1.82 (0.40), residues: 172 sheet: 0.31 (0.45), residues: 120 loop : 0.35 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 110 HIS 0.003 0.001 HIS A 84 PHE 0.006 0.001 PHE B 43 TYR 0.012 0.001 TYR A 62 ARG 0.001 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 210) hydrogen bonds : angle 4.31971 ( 582) SS BOND : bond 0.00073 ( 2) SS BOND : angle 0.66120 ( 4) covalent geometry : bond 0.00376 ( 3805) covalent geometry : angle 0.44647 ( 5134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8607 (m-40) cc_final: 0.8359 (m110) outliers start: 7 outliers final: 6 residues processed: 34 average time/residue: 0.1535 time to fit residues: 6.8645 Evaluate side-chains 34 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.192055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.107069 restraints weight = 3723.494| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.55 r_work: 0.2943 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3807 Z= 0.181 Angle : 0.457 5.704 5138 Z= 0.245 Chirality : 0.041 0.126 527 Planarity : 0.004 0.032 640 Dihedral : 11.946 147.150 594 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.43 % Allowed : 14.56 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.32 (0.40), residues: 450 helix: 1.77 (0.39), residues: 172 sheet: 0.47 (0.45), residues: 117 loop : 0.37 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 110 HIS 0.003 0.001 HIS A 84 PHE 0.007 0.001 PHE B 42 TYR 0.013 0.001 TYR A 62 ARG 0.001 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 210) hydrogen bonds : angle 4.36856 ( 582) SS BOND : bond 0.00055 ( 2) SS BOND : angle 0.67369 ( 4) covalent geometry : bond 0.00432 ( 3805) covalent geometry : angle 0.45719 ( 5134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8631 (m-40) cc_final: 0.8395 (m110) outliers start: 9 outliers final: 8 residues processed: 36 average time/residue: 0.1503 time to fit residues: 7.1114 Evaluate side-chains 35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.193382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.108512 restraints weight = 3716.148| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.55 r_work: 0.2962 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3807 Z= 0.150 Angle : 0.435 5.603 5138 Z= 0.233 Chirality : 0.040 0.124 527 Planarity : 0.003 0.032 640 Dihedral : 11.661 147.464 594 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.43 % Allowed : 14.29 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.50 (0.40), residues: 450 helix: 1.92 (0.39), residues: 172 sheet: 0.58 (0.45), residues: 117 loop : 0.45 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 110 HIS 0.003 0.001 HIS A 84 PHE 0.006 0.001 PHE B 43 TYR 0.012 0.001 TYR A 62 ARG 0.001 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 210) hydrogen bonds : angle 4.22168 ( 582) SS BOND : bond 0.00068 ( 2) SS BOND : angle 0.58837 ( 4) covalent geometry : bond 0.00354 ( 3805) covalent geometry : angle 0.43487 ( 5134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8582 (m-40) cc_final: 0.8345 (m110) outliers start: 9 outliers final: 8 residues processed: 37 average time/residue: 0.1443 time to fit residues: 6.9907 Evaluate side-chains 36 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 124 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.193518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.108444 restraints weight = 3770.987| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.56 r_work: 0.2961 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3807 Z= 0.148 Angle : 0.433 5.620 5138 Z= 0.231 Chirality : 0.040 0.126 527 Planarity : 0.003 0.032 640 Dihedral : 11.506 147.584 594 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.16 % Allowed : 14.56 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.57 (0.40), residues: 450 helix: 1.97 (0.39), residues: 172 sheet: 0.65 (0.46), residues: 118 loop : 0.48 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 110 HIS 0.003 0.001 HIS A 84 PHE 0.006 0.001 PHE B 43 TYR 0.012 0.001 TYR A 62 ARG 0.001 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 210) hydrogen bonds : angle 4.18359 ( 582) SS BOND : bond 0.00069 ( 2) SS BOND : angle 0.61183 ( 4) covalent geometry : bond 0.00349 ( 3805) covalent geometry : angle 0.43244 ( 5134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8590 (m-40) cc_final: 0.8324 (m110) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.1454 time to fit residues: 6.8511 Evaluate side-chains 35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 124 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 40 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.196459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.112743 restraints weight = 3675.549| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.56 r_work: 0.3008 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3807 Z= 0.093 Angle : 0.396 5.405 5138 Z= 0.210 Chirality : 0.038 0.118 527 Planarity : 0.003 0.031 640 Dihedral : 10.992 148.163 594 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.35 % Allowed : 14.82 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.92 (0.40), residues: 450 helix: 2.36 (0.39), residues: 172 sheet: 0.77 (0.45), residues: 118 loop : 0.60 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 110 HIS 0.001 0.001 HIS A 84 PHE 0.006 0.001 PHE B 43 TYR 0.008 0.001 TYR A 62 ARG 0.002 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.02941 ( 210) hydrogen bonds : angle 3.92047 ( 582) SS BOND : bond 0.00195 ( 2) SS BOND : angle 0.32091 ( 4) covalent geometry : bond 0.00210 ( 3805) covalent geometry : angle 0.39616 ( 5134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: D 97 LYS cc_start: 0.7333 (ptmm) cc_final: 0.7069 (ptmm) outliers start: 5 outliers final: 4 residues processed: 33 average time/residue: 0.1714 time to fit residues: 7.2871 Evaluate side-chains 32 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.196590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.112338 restraints weight = 3716.481| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.58 r_work: 0.3003 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3807 Z= 0.104 Angle : 0.401 5.410 5138 Z= 0.213 Chirality : 0.039 0.122 527 Planarity : 0.003 0.031 640 Dihedral : 10.894 148.360 594 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.08 % Allowed : 15.90 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.40), residues: 450 helix: 2.44 (0.39), residues: 172 sheet: 0.79 (0.45), residues: 118 loop : 0.64 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 110 HIS 0.002 0.001 HIS A 84 PHE 0.007 0.001 PHE B 43 TYR 0.010 0.001 TYR A 62 ARG 0.001 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 210) hydrogen bonds : angle 3.89733 ( 582) SS BOND : bond 0.00123 ( 2) SS BOND : angle 0.42804 ( 4) covalent geometry : bond 0.00237 ( 3805) covalent geometry : angle 0.40093 ( 5134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.387 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 32 average time/residue: 0.1569 time to fit residues: 6.6568 Evaluate side-chains 32 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.193876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108823 restraints weight = 3767.146| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.61 r_work: 0.2952 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3807 Z= 0.166 Angle : 0.438 5.624 5138 Z= 0.233 Chirality : 0.040 0.128 527 Planarity : 0.003 0.032 640 Dihedral : 11.365 147.642 594 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.08 % Allowed : 15.63 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.79 (0.40), residues: 450 helix: 2.18 (0.39), residues: 172 sheet: 0.68 (0.45), residues: 118 loop : 0.62 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 110 HIS 0.004 0.001 HIS A 84 PHE 0.007 0.001 PHE B 43 TYR 0.013 0.001 TYR A 62 ARG 0.001 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 210) hydrogen bonds : angle 4.14714 ( 582) SS BOND : bond 0.00048 ( 2) SS BOND : angle 0.64346 ( 4) covalent geometry : bond 0.00393 ( 3805) covalent geometry : angle 0.43813 ( 5134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3098.05 seconds wall clock time: 54 minutes 20.38 seconds (3260.38 seconds total)