Starting phenix.real_space_refine on Wed Jul 23 16:00:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw9_39626/07_2025/8yw9_39626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw9_39626/07_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_39626/07_2025/8yw9_39626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw9_39626/07_2025/8yw9_39626.map" model { file = "/net/cci-nas-00/data/ceres_data/8yw9_39626/07_2025/8yw9_39626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw9_39626/07_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-5711/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: 3.55, per 1000 atoms: 0.96 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: 1.04 Conformation dependent library (CDL) restraints added in 469.4 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: 0.54 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: 1.07 Time building geometry restraints manager: 1.22 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: 2.540 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.910 Find NCS groups from input model: 0.040 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.860 ------------------------------------------------------------------------------- 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 : 0.406 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: 0.2038 time to fit residues: 10.0371 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 : 0.405 ------------------------------------------------------------------------------- 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 = 51)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.112521 restraints weight = 3700.053| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.47 r_work: 0.2983 rms_B_bonded: 3.20 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: 0.7761 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 : 0.370 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8501 (m-40) cc_final: 0.8141 (m110) REVERT: B 86 SER cc_start: 0.9257 (p) cc_final: 0.8916 (m) outliers start: 10 outliers final: 6 residues processed: 39 average time/residue: 0.1516 time to fit residues: 7.6788 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 : 0.369 ------------------------------------------------------------------------------- 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: 0.8980 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.189075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.104333 restraints weight = 3760.228| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.55 r_work: 0.2903 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3807 Z= 0.291 Angle : 0.547 5.944 5138 Z= 0.293 Chirality : 0.045 0.143 527 Planarity : 0.004 0.033 640 Dihedral : 12.786 145.803 594 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.55 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: 0.44 (0.39), residues: 450 helix: 1.13 (0.39), residues: 172 sheet: -0.15 (0.43), residues: 120 loop : -0.08 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 110 HIS 0.006 0.002 HIS C 31 PHE 0.012 0.002 PHE A 69 TYR 0.014 0.002 TYR C 98 ARG 0.002 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 210) hydrogen bonds : angle 4.95096 ( 582) SS BOND : bond 0.00109 ( 2) SS BOND : angle 1.12426 ( 4) covalent geometry : bond 0.00702 ( 3805) covalent geometry : angle 0.54612 ( 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 43 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8737 (m-40) cc_final: 0.8491 (m110) outliers start: 12 outliers final: 10 residues processed: 39 average time/residue: 0.1451 time to fit residues: 7.4861 Evaluate side-chains 41 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 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: 20.0000 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.192758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.109336 restraints weight = 3692.990| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.54 r_work: 0.2947 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3807 Z= 0.175 Angle : 0.463 5.659 5138 Z= 0.249 Chirality : 0.041 0.120 527 Planarity : 0.004 0.028 640 Dihedral : 12.066 146.963 594 Min Nonbonded Distance : 2.397 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 (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: 0.92 (0.40), residues: 450 helix: 1.57 (0.40), residues: 172 sheet: 0.07 (0.44), residues: 120 loop : 0.16 (0.52), residues: 158 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 0.008 0.001 PHE A 69 TYR 0.013 0.001 TYR A 62 ARG 0.001 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 210) hydrogen bonds : angle 4.48935 ( 582) SS BOND : bond 0.00095 ( 2) SS BOND : angle 0.74141 ( 4) covalent geometry : bond 0.00417 ( 3805) covalent geometry : angle 0.46277 ( 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 37 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8673 (m-40) cc_final: 0.8419 (m110) REVERT: B 86 SER cc_start: 0.9280 (p) cc_final: 0.8936 (m) REVERT: D 47 TRP cc_start: 0.7094 (t60) cc_final: 0.6798 (t60) outliers start: 9 outliers final: 6 residues processed: 35 average time/residue: 0.1457 time to fit residues: 6.7610 Evaluate side-chains 33 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 21 SER Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 124 THR 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: 0.7980 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 22 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.196085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.111793 restraints weight = 3791.282| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.60 r_work: 0.2985 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1967 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= 0.112 Angle : 0.416 5.450 5138 Z= 0.223 Chirality : 0.039 0.122 527 Planarity : 0.003 0.028 640 Dihedral : 11.513 147.846 594 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.35 % Allowed : 14.56 % 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: 1.45 (0.40), residues: 450 helix: 2.01 (0.40), residues: 172 sheet: 0.38 (0.45), residues: 120 loop : 0.42 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 47 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 0.03111 ( 210) hydrogen bonds : angle 4.13310 ( 582) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.46650 ( 4) covalent geometry : bond 0.00255 ( 3805) covalent geometry : angle 0.41592 ( 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: 5 poor density : 31 time to evaluate : 0.411 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 34 average time/residue: 0.1692 time to fit residues: 7.4789 Evaluate side-chains 33 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.189569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.104520 restraints weight = 3743.955| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.56 r_work: 0.2903 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3807 Z= 0.285 Angle : 0.519 5.983 5138 Z= 0.277 Chirality : 0.044 0.132 527 Planarity : 0.004 0.033 640 Dihedral : 12.379 145.172 594 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.16 % Allowed : 14.82 % 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: 1.06 (0.40), residues: 450 helix: 1.54 (0.39), residues: 172 sheet: 0.28 (0.45), residues: 120 loop : 0.30 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.004 0.001 HIS A 84 PHE 0.011 0.002 PHE A 81 TYR 0.013 0.002 TYR A 62 ARG 0.002 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 210) hydrogen bonds : angle 4.63068 ( 582) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.97558 ( 4) covalent geometry : bond 0.00685 ( 3805) covalent geometry : angle 0.51835 ( 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: 8 poor density : 29 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8676 (m110) cc_final: 0.8431 (m110) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.1391 time to fit residues: 6.8356 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 : 0.385 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 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 = 0.4083 r_free = 0.4083 target = 0.194946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110864 restraints weight = 3714.613| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.53 r_work: 0.2993 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2121 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= 0.111 Angle : 0.415 5.439 5138 Z= 0.222 Chirality : 0.039 0.120 527 Planarity : 0.003 0.030 640 Dihedral : 11.530 147.833 594 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.81 % Allowed : 15.09 % 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: 1.58 (0.40), residues: 450 helix: 2.01 (0.40), residues: 172 sheet: 0.61 (0.45), residues: 117 loop : 0.47 (0.52), residues: 161 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 0.002 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03086 ( 210) hydrogen bonds : angle 4.07892 ( 582) SS BOND : bond 0.00146 ( 2) SS BOND : angle 0.41383 ( 4) covalent geometry : bond 0.00254 ( 3805) covalent geometry : angle 0.41478 ( 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 33 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8565 (m110) cc_final: 0.8236 (m-40) outliers start: 3 outliers final: 3 residues processed: 33 average time/residue: 0.1650 time to fit residues: 7.0662 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 : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 25 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 43 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.194974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.111874 restraints weight = 3737.822| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.49 r_work: 0.2998 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3807 Z= 0.111 Angle : 0.410 5.438 5138 Z= 0.219 Chirality : 0.039 0.120 527 Planarity : 0.003 0.031 640 Dihedral : 11.250 148.096 594 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.62 % Allowed : 15.09 % 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: 1.84 (0.40), residues: 450 helix: 2.25 (0.39), residues: 172 sheet: 0.77 (0.45), residues: 117 loop : 0.56 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 50 HIS 0.003 0.001 HIS A 84 PHE 0.006 0.001 PHE B 43 TYR 0.011 0.001 TYR A 62 ARG 0.001 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 210) hydrogen bonds : angle 3.98197 ( 582) SS BOND : bond 0.00122 ( 2) SS BOND : angle 0.40048 ( 4) covalent geometry : bond 0.00254 ( 3805) covalent geometry : angle 0.41004 ( 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 36 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8624 (m110) cc_final: 0.8280 (m-40) outliers start: 6 outliers final: 5 residues processed: 36 average time/residue: 0.1654 time to fit residues: 7.7889 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 : 0.405 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 42 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 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 = 0.4099 r_free = 0.4099 target = 0.196491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.112035 restraints weight = 3672.910| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.60 r_work: 0.2995 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3807 Z= 0.107 Angle : 0.406 5.414 5138 Z= 0.216 Chirality : 0.039 0.121 527 Planarity : 0.003 0.031 640 Dihedral : 10.975 148.172 594 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: 1.99 (0.40), residues: 450 helix: 2.38 (0.39), residues: 172 sheet: 0.85 (0.45), residues: 118 loop : 0.65 (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 0.006 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 0.03037 ( 210) hydrogen bonds : angle 3.93018 ( 582) SS BOND : bond 0.00125 ( 2) SS BOND : angle 0.41015 ( 4) covalent geometry : bond 0.00244 ( 3805) covalent geometry : angle 0.40638 ( 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 33 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8633 (m110) cc_final: 0.8282 (m-40) outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.1455 time to fit residues: 6.3462 Evaluate side-chains 33 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 41 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.198195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.114546 restraints weight = 3716.989| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.64 r_work: 0.2988 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3807 Z= 0.109 Angle : 0.408 5.428 5138 Z= 0.216 Chirality : 0.039 0.119 527 Planarity : 0.003 0.030 640 Dihedral : 10.796 148.324 594 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: 2.09 (0.40), residues: 450 helix: 2.44 (0.39), residues: 172 sheet: 0.89 (0.45), residues: 118 loop : 0.75 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 50 HIS 0.003 0.001 HIS A 84 PHE 0.006 0.001 PHE B 43 TYR 0.011 0.001 TYR A 62 ARG 0.001 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03069 ( 210) hydrogen bonds : angle 3.88661 ( 582) SS BOND : bond 0.00102 ( 2) SS BOND : angle 0.50104 ( 4) covalent geometry : bond 0.00250 ( 3805) covalent geometry : angle 0.40749 ( 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 34 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8616 (m110) cc_final: 0.8275 (m-40) outliers start: 4 outliers final: 4 residues processed: 34 average time/residue: 0.1514 time to fit residues: 6.9346 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 : 0.409 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 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 = 0.4103 r_free = 0.4103 target = 0.195669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.111612 restraints weight = 3765.932| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.63 r_work: 0.2947 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2296 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= 0.165 Angle : 0.441 5.595 5138 Z= 0.234 Chirality : 0.040 0.127 527 Planarity : 0.003 0.031 640 Dihedral : 11.285 147.684 594 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.35 % Allowed : 15.09 % Favored : 83.56 % 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: 1.85 (0.40), residues: 450 helix: 2.18 (0.39), residues: 172 sheet: 0.73 (0.45), residues: 118 loop : 0.72 (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 0.006 0.001 PHE A 69 TYR 0.013 0.001 TYR A 62 ARG 0.001 0.000 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 210) hydrogen bonds : angle 4.12654 ( 582) SS BOND : bond 0.00024 ( 2) SS BOND : angle 0.75572 ( 4) covalent geometry : bond 0.00392 ( 3805) covalent geometry : angle 0.44094 ( 5134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3293.13 seconds wall clock time: 56 minutes 42.70 seconds (3402.70 seconds total)