Starting phenix.real_space_refine on Wed Sep 17 04:01:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw9_39626/09_2025/8yw9_39626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw9_39626/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yw9_39626/09_2025/8yw9_39626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw9_39626/09_2025/8yw9_39626.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yw9_39626/09_2025/8yw9_39626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw9_39626/09_2025/8yw9_39626.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.24, per 1000 atoms: 0.33 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: 0.34 Conformation dependent library (CDL) restraints added in 163.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.16 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: 0.57 Time building geometry restraints manager: 0.42 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.990 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.700 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (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 ARG 0.002 0.000 ARG C 72 TYR 0.014 0.001 TYR A 62 PHE 0.011 0.002 PHE A 81 TRP 0.007 0.001 TRP B 82 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00972 ( 3805) covalent geometry : angle 0.94199 ( 5134) SS BOND : bond 0.00462 ( 2) SS BOND : angle 3.20884 ( 4) hydrogen bonds : bond 0.13872 ( 210) hydrogen bonds : angle 6.56224 ( 582) *********************** 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 : 0.135 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: 0.0932 time to fit residues: 4.5545 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 : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.193822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111181 restraints weight = 3774.288| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.49 r_work: 0.2965 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3807 Z= 0.174 Angle : 0.493 5.541 5138 Z= 0.266 Chirality : 0.041 0.127 527 Planarity : 0.004 0.035 640 Dihedral : 12.816 147.160 594 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.43 % Allowed : 12.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.39), residues: 450 helix: 1.16 (0.40), residues: 171 sheet: -0.23 (0.41), residues: 133 loop : 0.01 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 50 TYR 0.020 0.001 TYR C 98 PHE 0.009 0.001 PHE A 69 TRP 0.006 0.001 TRP A 28 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 3805) covalent geometry : angle 0.49296 ( 5134) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.74490 ( 4) hydrogen bonds : bond 0.03648 ( 210) hydrogen bonds : angle 4.87242 ( 582) *********************** 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 41 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8576 (m-40) cc_final: 0.8220 (m110) REVERT: B 86 SER cc_start: 0.9260 (p) cc_final: 0.8937 (m) outliers start: 9 outliers final: 7 residues processed: 39 average time/residue: 0.0647 time to fit residues: 3.2301 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 : 0.157 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.194892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111613 restraints weight = 3733.001| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.56 r_work: 0.2978 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1614 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= 0.132 Angle : 0.436 5.498 5138 Z= 0.234 Chirality : 0.039 0.122 527 Planarity : 0.003 0.026 640 Dihedral : 12.043 148.658 594 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.89 % Allowed : 13.75 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.40), residues: 450 helix: 1.70 (0.40), residues: 172 sheet: 0.21 (0.43), residues: 120 loop : 0.15 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 72 TYR 0.012 0.001 TYR C 98 PHE 0.007 0.001 PHE B 43 TRP 0.005 0.001 TRP C 110 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3805) covalent geometry : angle 0.43611 ( 5134) SS BOND : bond 0.00087 ( 2) SS BOND : angle 0.67305 ( 4) hydrogen bonds : bond 0.03326 ( 210) hydrogen bonds : angle 4.42559 ( 582) *********************** 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 35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8629 (m-40) cc_final: 0.8350 (m110) REVERT: C 69 THR cc_start: 0.8239 (m) cc_final: 0.8014 (m) outliers start: 7 outliers final: 5 residues processed: 33 average time/residue: 0.0706 time to fit residues: 3.1039 Evaluate side-chains 33 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 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 28 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4094 r_free = 0.4094 target = 0.195318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110930 restraints weight = 3714.149| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.60 r_work: 0.2960 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3807 Z= 0.148 Angle : 0.441 5.564 5138 Z= 0.236 Chirality : 0.040 0.125 527 Planarity : 0.003 0.026 640 Dihedral : 11.724 147.627 594 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.16 % Allowed : 13.48 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.40), residues: 450 helix: 1.84 (0.40), residues: 172 sheet: 0.33 (0.45), residues: 120 loop : 0.35 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 68 TYR 0.012 0.001 TYR A 62 PHE 0.006 0.001 PHE A 69 TRP 0.005 0.001 TRP A 28 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 3805) covalent geometry : angle 0.44090 ( 5134) SS BOND : bond 0.00079 ( 2) SS BOND : angle 0.76978 ( 4) hydrogen bonds : bond 0.03374 ( 210) hydrogen bonds : angle 4.29536 ( 582) *********************** 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 37 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8652 (m-40) cc_final: 0.8413 (m110) outliers start: 8 outliers final: 6 residues processed: 35 average time/residue: 0.0744 time to fit residues: 3.2941 Evaluate side-chains 35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.193610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108954 restraints weight = 3723.375| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.58 r_work: 0.2959 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1908 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= 0.154 Angle : 0.438 5.621 5138 Z= 0.234 Chirality : 0.040 0.122 527 Planarity : 0.003 0.029 640 Dihedral : 11.737 147.603 594 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.43 % Allowed : 13.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.40), residues: 450 helix: 1.91 (0.39), residues: 172 sheet: 0.47 (0.45), residues: 120 loop : 0.46 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 68 TYR 0.012 0.001 TYR A 62 PHE 0.006 0.001 PHE A 69 TRP 0.005 0.001 TRP C 110 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 3805) covalent geometry : angle 0.43720 ( 5134) SS BOND : bond 0.00058 ( 2) SS BOND : angle 0.75080 ( 4) hydrogen bonds : bond 0.03380 ( 210) hydrogen bonds : angle 4.24470 ( 582) *********************** 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: 9 poor density : 27 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8662 (m-40) cc_final: 0.8423 (m110) outliers start: 9 outliers final: 8 residues processed: 36 average time/residue: 0.0780 time to fit residues: 3.5617 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 : 0.149 ------------------------------------------------------------------------------- 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 124 THR Chi-restraints excluded: chain D residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.197079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.114349 restraints weight = 3771.475| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.60 r_work: 0.2983 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3807 Z= 0.121 Angle : 0.414 5.504 5138 Z= 0.221 Chirality : 0.039 0.121 527 Planarity : 0.003 0.030 640 Dihedral : 11.438 147.859 594 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.35 % Allowed : 15.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.40), residues: 450 helix: 2.15 (0.39), residues: 172 sheet: 0.72 (0.46), residues: 120 loop : 0.57 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 72 TYR 0.010 0.001 TYR A 62 PHE 0.006 0.001 PHE B 43 TRP 0.005 0.001 TRP C 110 HIS 0.002 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3805) covalent geometry : angle 0.41342 ( 5134) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.59525 ( 4) hydrogen bonds : bond 0.03155 ( 210) hydrogen bonds : angle 4.05833 ( 582) *********************** 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 32 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8630 (m-40) cc_final: 0.8422 (m110) REVERT: D 97 LYS cc_start: 0.7700 (tttp) cc_final: 0.7415 (tttp) outliers start: 5 outliers final: 3 residues processed: 32 average time/residue: 0.0738 time to fit residues: 2.9521 Evaluate side-chains 30 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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 25 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.196344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111791 restraints weight = 3818.251| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.62 r_work: 0.2992 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3807 Z= 0.106 Angle : 0.402 5.437 5138 Z= 0.215 Chirality : 0.039 0.124 527 Planarity : 0.003 0.030 640 Dihedral : 11.130 148.130 594 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.81 % Allowed : 15.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.40), residues: 450 helix: 2.34 (0.39), residues: 172 sheet: 0.87 (0.46), residues: 117 loop : 0.65 (0.53), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 72 TYR 0.010 0.001 TYR A 62 PHE 0.006 0.001 PHE B 43 TRP 0.005 0.001 TRP C 110 HIS 0.002 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3805) covalent geometry : angle 0.40218 ( 5134) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.46821 ( 4) hydrogen bonds : bond 0.03034 ( 210) hydrogen bonds : angle 3.91343 ( 582) *********************** 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 33 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8619 (m-40) cc_final: 0.8404 (m110) outliers start: 3 outliers final: 3 residues processed: 33 average time/residue: 0.0795 time to fit residues: 3.3481 Evaluate side-chains 33 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 124 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 2 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.196030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111632 restraints weight = 3798.659| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.61 r_work: 0.2990 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3807 Z= 0.112 Angle : 0.405 5.465 5138 Z= 0.216 Chirality : 0.039 0.123 527 Planarity : 0.003 0.030 640 Dihedral : 10.970 148.171 594 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.40), residues: 450 helix: 2.41 (0.39), residues: 172 sheet: 1.02 (0.46), residues: 117 loop : 0.70 (0.53), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 84 TYR 0.011 0.001 TYR A 62 PHE 0.006 0.001 PHE B 43 TRP 0.005 0.001 TRP C 110 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3805) covalent geometry : angle 0.40529 ( 5134) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.38651 ( 4) hydrogen bonds : bond 0.03078 ( 210) hydrogen bonds : angle 3.89913 ( 582) *********************** 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 34 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8615 (m-40) cc_final: 0.8389 (m110) outliers start: 4 outliers final: 4 residues processed: 34 average time/residue: 0.0730 time to fit residues: 3.1659 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 : 0.133 ------------------------------------------------------------------------------- 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 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 43 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.195402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110799 restraints weight = 3771.528| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.63 r_work: 0.2970 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2251 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= 0.136 Angle : 0.416 5.551 5138 Z= 0.222 Chirality : 0.039 0.124 527 Planarity : 0.003 0.031 640 Dihedral : 11.122 147.879 594 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.35 % Allowed : 15.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.40), residues: 450 helix: 2.28 (0.39), residues: 172 sheet: 0.93 (0.45), residues: 118 loop : 0.77 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 10 TYR 0.012 0.001 TYR A 62 PHE 0.006 0.001 PHE B 43 TRP 0.005 0.001 TRP C 110 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 3805) covalent geometry : angle 0.41554 ( 5134) SS BOND : bond 0.00119 ( 2) SS BOND : angle 0.50882 ( 4) hydrogen bonds : bond 0.03216 ( 210) hydrogen bonds : angle 3.98766 ( 582) *********************** 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 : 0.135 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8608 (m-40) cc_final: 0.8384 (m110) outliers start: 5 outliers final: 5 residues processed: 34 average time/residue: 0.0673 time to fit residues: 3.0209 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 : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 87 LEU 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 4 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.195525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.111383 restraints weight = 3815.469| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.55 r_work: 0.2995 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3807 Z= 0.117 Angle : 0.403 5.484 5138 Z= 0.215 Chirality : 0.039 0.118 527 Planarity : 0.003 0.030 640 Dihedral : 10.965 148.065 594 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.62 % Allowed : 15.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.40), residues: 450 helix: 2.39 (0.39), residues: 172 sheet: 0.94 (0.45), residues: 118 loop : 0.82 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 72 TYR 0.011 0.001 TYR A 62 PHE 0.005 0.001 PHE B 43 TRP 0.005 0.001 TRP C 110 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3805) covalent geometry : angle 0.40278 ( 5134) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.46263 ( 4) hydrogen bonds : bond 0.03097 ( 210) hydrogen bonds : angle 3.89714 ( 582) ********************** 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 35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8585 (m-40) cc_final: 0.8364 (m110) outliers start: 6 outliers final: 6 residues processed: 35 average time/residue: 0.0717 time to fit residues: 3.2383 Evaluate side-chains 35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.0020 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.197510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.114998 restraints weight = 3681.019| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.53 r_work: 0.3031 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2475 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= 0.087 Angle : 0.383 5.386 5138 Z= 0.203 Chirality : 0.038 0.115 527 Planarity : 0.003 0.030 640 Dihedral : 10.559 148.384 594 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.08 % Allowed : 16.17 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.40), residues: 450 helix: 2.61 (0.39), residues: 172 sheet: 0.97 (0.45), residues: 118 loop : 0.91 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 72 TYR 0.009 0.001 TYR A 62 PHE 0.006 0.001 PHE A 66 TRP 0.005 0.001 TRP C 110 HIS 0.001 0.000 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 3805) covalent geometry : angle 0.38271 ( 5134) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.32197 ( 4) hydrogen bonds : bond 0.02857 ( 210) hydrogen bonds : angle 3.71117 ( 582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1621.11 seconds wall clock time: 28 minutes 30.07 seconds (1710.07 seconds total)