Starting phenix.real_space_refine on Sat Apr 26 17:06:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9knx_62465/04_2025/9knx_62465.cif Found real_map, /net/cci-nas-00/data/ceres_data/9knx_62465/04_2025/9knx_62465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9knx_62465/04_2025/9knx_62465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9knx_62465/04_2025/9knx_62465.map" model { file = "/net/cci-nas-00/data/ceres_data/9knx_62465/04_2025/9knx_62465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9knx_62465/04_2025/9knx_62465.cif" } resolution = 3.72 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= 0.016 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 17 5.16 5 C 1736 2.51 5 N 452 2.21 5 O 468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2675 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1000 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Chain: "A" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 707 Classifications: {'peptide': 89} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 84} Chain: "C" 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: 2.98, per 1000 atoms: 1.11 Number of scatterers: 2675 At special positions: 0 Unit cell: (79.23, 66.69, 95.19, 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 17 16.00 P 2 15.00 O 468 8.00 N 452 7.00 C 1736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 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: 0.73 Conformation dependent library (CDL) restraints added in 304.8 milliseconds 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 606 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 3 sheets defined 59.9% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 40 through 60 removed outlier: 4.267A pdb=" N TRP B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Proline residue: B 46 - end of helix removed outlier: 3.824A pdb=" N GLY B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU B 52 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 87 removed outlier: 3.555A pdb=" N LEU B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 127 removed outlier: 3.580A pdb=" N PHE B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.963A pdb=" N PHE A 27 " --> pdb=" O MET A 23 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TRP A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY A 29 " --> pdb=" O THR A 25 " (cutoff:3.500A) Proline residue: A 30 - end of helix Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.626A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 77 through 108 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' 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: 6.404A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.634A 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: 6.404A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) 172 hydrogen bonds defined for protein. 480 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: 0.67 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 399 1.30 - 1.43: 761 1.43 - 1.56: 1540 1.56 - 1.69: 14 1.69 - 1.81: 28 Bond restraints: 2742 Sorted by residual: bond pdb=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 1.334 1.435 -0.101 1.10e-02 8.26e+03 8.42e+01 bond pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 1.334 1.432 -0.098 1.10e-02 8.26e+03 7.86e+01 bond pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 1.342 1.441 -0.099 1.50e-02 4.44e+03 4.36e+01 bond pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 1.342 1.436 -0.094 1.50e-02 4.44e+03 3.93e+01 bond pdb=" OB2 CDL B 201 " pdb=" PB2 CDL B 201 " ideal model delta sigma weight residual 1.579 1.670 -0.091 1.50e-02 4.44e+03 3.65e+01 ... (remaining 2737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 3422 1.88 - 3.76: 231 3.76 - 5.64: 30 5.64 - 7.53: 5 7.53 - 9.41: 6 Bond angle restraints: 3694 Sorted by residual: angle pdb=" C51 CDL B 201 " pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 111.33 119.43 -8.10 1.32e+00 5.72e-01 3.75e+01 angle pdb=" C11 CDL B 201 " pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 111.33 119.40 -8.07 1.32e+00 5.72e-01 3.72e+01 angle pdb=" C71 CDL B 201 " pdb=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 111.64 120.73 -9.09 1.65e+00 3.69e-01 3.05e+01 angle pdb=" C31 CDL B 201 " pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 111.64 120.52 -8.88 1.65e+00 3.69e-01 2.91e+01 angle pdb=" CA3 CDL B 201 " pdb=" OA5 CDL B 201 " pdb=" PA1 CDL B 201 " ideal model delta sigma weight residual 121.27 116.53 4.74 1.00e+00 1.00e+00 2.25e+01 ... (remaining 3689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 1427 16.12 - 32.24: 134 32.24 - 48.35: 52 48.35 - 64.47: 25 64.47 - 80.59: 4 Dihedral angle restraints: 1642 sinusoidal: 695 harmonic: 947 Sorted by residual: dihedral pdb=" C THR A 56 " pdb=" N THR A 56 " pdb=" CA THR A 56 " pdb=" CB THR A 56 " ideal model delta harmonic sigma weight residual -122.00 -130.90 8.90 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" C PHE A 27 " pdb=" N PHE A 27 " pdb=" CA PHE A 27 " pdb=" CB PHE A 27 " ideal model delta harmonic sigma weight residual -122.60 -130.64 8.04 0 2.50e+00 1.60e-01 1.03e+01 dihedral pdb=" N ASN B 33 " pdb=" CA ASN B 33 " pdb=" CB ASN B 33 " pdb=" CG ASN B 33 " ideal model delta sinusoidal sigma weight residual -60.00 -119.74 59.74 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 272 0.052 - 0.104: 78 0.104 - 0.155: 24 0.155 - 0.207: 9 0.207 - 0.259: 4 Chirality restraints: 387 Sorted by residual: chirality pdb=" CA VAL C 98 " pdb=" N VAL C 98 " pdb=" C VAL C 98 " pdb=" CB VAL C 98 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA PHE A 27 " pdb=" N PHE A 27 " pdb=" C PHE A 27 " pdb=" CB PHE A 27 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB VAL A 73 " pdb=" CA VAL A 73 " pdb=" CG1 VAL A 73 " pdb=" CG2 VAL A 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 384 not shown) Planarity restraints: 454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 50 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" C ALA C 50 " 0.052 2.00e-02 2.50e+03 pdb=" O ALA C 50 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE C 51 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 54 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C ARG A 54 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG A 54 " 0.013 2.00e-02 2.50e+03 pdb=" N MET A 55 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 71 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C GLN B 71 " 0.030 2.00e-02 2.50e+03 pdb=" O GLN B 71 " -0.011 2.00e-02 2.50e+03 pdb=" N SER B 72 " -0.011 2.00e-02 2.50e+03 ... (remaining 451 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 558 2.78 - 3.31: 2471 3.31 - 3.84: 4368 3.84 - 4.37: 5125 4.37 - 4.90: 8531 Nonbonded interactions: 21053 Sorted by model distance: nonbonded pdb=" O CYS A 60 " pdb=" OG SER A 63 " model vdw 2.250 3.040 nonbonded pdb=" O LEU B 22 " pdb=" NH2 ARG B 29 " model vdw 2.284 3.120 nonbonded pdb=" NZ LYS B 49 " pdb=" OD1 ASN B 100 " model vdw 2.297 3.120 nonbonded pdb=" OD2 ASP B 59 " pdb=" OG SER A 52 " model vdw 2.299 3.040 nonbonded pdb=" OA6 CDL B 201 " pdb=" OA8 CDL B 201 " model vdw 2.400 2.432 ... (remaining 21048 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.230 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 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 : 0.011 0.105 2743 Z= 0.689 Angle : 1.060 9.408 3696 Z= 0.697 Chirality : 0.062 0.259 387 Planarity : 0.005 0.036 454 Dihedral : 16.420 80.590 1033 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.38 % Allowed : 7.89 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.44), residues: 323 helix: -1.31 (0.33), residues: 168 sheet: 0.03 (0.62), residues: 66 loop : -0.50 (0.75), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 44 HIS 0.004 0.001 HIS A 84 PHE 0.020 0.002 PHE A 69 TYR 0.014 0.001 TYR B 85 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.12628 ( 168) hydrogen bonds : angle 6.50125 ( 480) SS BOND : bond 0.00748 ( 1) SS BOND : angle 4.47585 ( 2) covalent geometry : bond 0.01108 ( 2742) covalent geometry : angle 1.05526 ( 3694) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: B 27 LYS cc_start: 0.8347 (mttt) cc_final: 0.8123 (tttt) REVERT: A 72 LYS cc_start: 0.7641 (tptt) cc_final: 0.7359 (tptt) REVERT: C 60 TYR cc_start: 0.7520 (m-80) cc_final: 0.7140 (m-80) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.1708 time to fit residues: 12.0084 Evaluate side-chains 48 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.0040 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN ** A 84 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 = 0.4376 r_free = 0.4376 target = 0.226613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.180578 restraints weight = 3310.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.185989 restraints weight = 2056.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.189771 restraints weight = 1499.733| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2743 Z= 0.142 Angle : 0.564 9.148 3696 Z= 0.294 Chirality : 0.041 0.160 387 Planarity : 0.005 0.045 454 Dihedral : 13.106 67.966 443 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.50 % Allowed : 12.78 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.36 (0.46), residues: 323 helix: 0.77 (0.39), residues: 167 sheet: 0.12 (0.60), residues: 65 loop : -0.42 (0.69), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 50 HIS 0.002 0.001 HIS A 84 PHE 0.010 0.001 PHE A 57 TYR 0.015 0.001 TYR B 85 ARG 0.002 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.04959 ( 168) hydrogen bonds : angle 4.90507 ( 480) SS BOND : bond 0.00084 ( 1) SS BOND : angle 0.53087 ( 2) covalent geometry : bond 0.00307 ( 2742) covalent geometry : angle 0.56448 ( 3694) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: B 27 LYS cc_start: 0.8487 (mttt) cc_final: 0.8279 (ttmm) REVERT: A 72 LYS cc_start: 0.7786 (tptt) cc_final: 0.7252 (tptt) REVERT: A 103 MET cc_start: 0.4511 (ptm) cc_final: 0.4296 (ptm) REVERT: C 60 TYR cc_start: 0.7963 (m-80) cc_final: 0.7289 (m-80) outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.1655 time to fit residues: 9.6381 Evaluate side-chains 48 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain A residue 23 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.224294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.180625 restraints weight = 3209.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.185902 restraints weight = 1997.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.189701 restraints weight = 1442.629| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2743 Z= 0.132 Angle : 0.504 7.377 3696 Z= 0.266 Chirality : 0.040 0.137 387 Planarity : 0.004 0.046 454 Dihedral : 11.307 57.067 443 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.88 % Allowed : 12.78 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.36 (0.48), residues: 323 helix: 1.77 (0.41), residues: 165 sheet: 0.40 (0.60), residues: 64 loop : -0.17 (0.69), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.002 0.001 HIS A 84 PHE 0.010 0.002 PHE A 57 TYR 0.014 0.001 TYR B 85 ARG 0.003 0.000 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 168) hydrogen bonds : angle 4.33975 ( 480) SS BOND : bond 0.00019 ( 1) SS BOND : angle 0.37241 ( 2) covalent geometry : bond 0.00285 ( 2742) covalent geometry : angle 0.50387 ( 3694) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: B 23 MET cc_start: 0.7970 (tpp) cc_final: 0.7389 (mpp) REVERT: B 27 LYS cc_start: 0.8555 (mttt) cc_final: 0.8284 (ttmm) REVERT: B 62 ARG cc_start: 0.7162 (ttt180) cc_final: 0.6888 (ttp-170) REVERT: A 72 LYS cc_start: 0.7938 (tptt) cc_final: 0.7338 (tptt) REVERT: A 103 MET cc_start: 0.4420 (ptm) cc_final: 0.4189 (ptm) REVERT: C 60 TYR cc_start: 0.7925 (m-80) cc_final: 0.7346 (m-80) outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 0.1801 time to fit residues: 11.2813 Evaluate side-chains 52 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain A residue 38 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 25 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 2 optimal weight: 0.0770 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.4361 r_free = 0.4361 target = 0.226652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.184439 restraints weight = 3227.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.189961 restraints weight = 1953.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.193912 restraints weight = 1386.536| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2743 Z= 0.112 Angle : 0.502 9.167 3696 Z= 0.256 Chirality : 0.039 0.141 387 Planarity : 0.004 0.047 454 Dihedral : 9.908 55.920 443 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.88 % Allowed : 14.29 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.77 (0.48), residues: 323 helix: 2.30 (0.41), residues: 165 sheet: 0.35 (0.59), residues: 68 loop : -0.24 (0.71), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 78 HIS 0.002 0.000 HIS A 84 PHE 0.007 0.001 PHE C 68 TYR 0.011 0.001 TYR B 85 ARG 0.002 0.000 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 168) hydrogen bonds : angle 4.11014 ( 480) SS BOND : bond 0.00295 ( 1) SS BOND : angle 0.06773 ( 2) covalent geometry : bond 0.00236 ( 2742) covalent geometry : angle 0.50253 ( 3694) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 MET cc_start: 0.7957 (tpp) cc_final: 0.7409 (mpp) REVERT: B 27 LYS cc_start: 0.8534 (mttt) cc_final: 0.8309 (ttmm) REVERT: A 103 MET cc_start: 0.4510 (ptm) cc_final: 0.4255 (ptm) REVERT: C 60 TYR cc_start: 0.7793 (m-80) cc_final: 0.7147 (m-80) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.1851 time to fit residues: 11.5194 Evaluate side-chains 52 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain A residue 93 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.0020 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 0.0170 chunk 7 optimal weight: 0.9990 overall best weight: 1.0030 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.208163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.163497 restraints weight = 3157.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.168292 restraints weight = 2010.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.171781 restraints weight = 1470.891| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2743 Z= 0.153 Angle : 0.530 7.003 3696 Z= 0.276 Chirality : 0.041 0.139 387 Planarity : 0.004 0.047 454 Dihedral : 9.958 57.438 443 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.63 % Allowed : 16.54 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.48), residues: 323 helix: 2.37 (0.41), residues: 165 sheet: 0.46 (0.63), residues: 61 loop : -0.09 (0.68), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 84 PHE 0.015 0.002 PHE C 68 TYR 0.014 0.001 TYR B 85 ARG 0.002 0.000 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.04731 ( 168) hydrogen bonds : angle 4.18322 ( 480) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.37533 ( 2) covalent geometry : bond 0.00346 ( 2742) covalent geometry : angle 0.53010 ( 3694) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 LYS cc_start: 0.8518 (mttt) cc_final: 0.8268 (ttmm) REVERT: B 62 ARG cc_start: 0.7194 (ttp-170) cc_final: 0.6882 (ttp-170) REVERT: A 103 MET cc_start: 0.4671 (ptm) cc_final: 0.4390 (ptm) REVERT: C 60 TYR cc_start: 0.7841 (m-80) cc_final: 0.7245 (m-80) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.1826 time to fit residues: 11.5912 Evaluate side-chains 55 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 93 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.221736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.179033 restraints weight = 3257.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.184109 restraints weight = 2075.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.187545 restraints weight = 1522.887| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2743 Z= 0.122 Angle : 0.495 6.141 3696 Z= 0.258 Chirality : 0.040 0.127 387 Planarity : 0.004 0.046 454 Dihedral : 9.503 59.975 443 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.26 % Allowed : 16.92 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.89 (0.48), residues: 323 helix: 2.44 (0.40), residues: 165 sheet: 0.17 (0.60), residues: 65 loop : -0.04 (0.71), residues: 93 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 0.016 0.001 PHE C 68 TYR 0.012 0.001 TYR B 85 ARG 0.002 0.000 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.04408 ( 168) hydrogen bonds : angle 4.06615 ( 480) SS BOND : bond 0.00150 ( 1) SS BOND : angle 0.26805 ( 2) covalent geometry : bond 0.00267 ( 2742) covalent geometry : angle 0.49491 ( 3694) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 LYS cc_start: 0.8518 (mttt) cc_final: 0.8301 (ttmm) REVERT: B 62 ARG cc_start: 0.7137 (ttp-170) cc_final: 0.6845 (ttp-170) REVERT: A 103 MET cc_start: 0.4669 (ptm) cc_final: 0.4450 (ptm) REVERT: C 52 ASP cc_start: 0.8559 (m-30) cc_final: 0.8246 (m-30) REVERT: C 60 TYR cc_start: 0.7701 (m-80) cc_final: 0.7105 (m-80) outliers start: 6 outliers final: 6 residues processed: 56 average time/residue: 0.1741 time to fit residues: 11.5000 Evaluate side-chains 58 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 93 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.0470 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 30.0000 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.4325 r_free = 0.4325 target = 0.221422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.178860 restraints weight = 3316.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.183320 restraints weight = 2098.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.187191 restraints weight = 1554.993| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2743 Z= 0.123 Angle : 0.486 6.121 3696 Z= 0.257 Chirality : 0.039 0.116 387 Planarity : 0.004 0.046 454 Dihedral : 9.225 54.748 443 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.63 % Allowed : 17.29 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.05 (0.48), residues: 323 helix: 2.54 (0.40), residues: 165 sheet: 0.21 (0.61), residues: 65 loop : 0.14 (0.72), residues: 93 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 0.009 0.001 PHE C 68 TYR 0.012 0.001 TYR B 85 ARG 0.003 0.000 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 168) hydrogen bonds : angle 4.02134 ( 480) SS BOND : bond 0.00133 ( 1) SS BOND : angle 0.31383 ( 2) covalent geometry : bond 0.00269 ( 2742) covalent geometry : angle 0.48579 ( 3694) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: B 27 LYS cc_start: 0.8546 (mttt) cc_final: 0.8345 (ttmm) REVERT: B 62 ARG cc_start: 0.7114 (ttp-170) cc_final: 0.6851 (ttp-170) REVERT: A 72 LYS cc_start: 0.8113 (tptt) cc_final: 0.7405 (tptt) REVERT: A 103 MET cc_start: 0.4709 (ptm) cc_final: 0.4482 (ptm) REVERT: C 7 SER cc_start: 0.8713 (t) cc_final: 0.8486 (p) REVERT: C 52 ASP cc_start: 0.8550 (m-30) cc_final: 0.8221 (m-30) REVERT: C 60 TYR cc_start: 0.7690 (m-80) cc_final: 0.7139 (m-80) outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 0.1638 time to fit residues: 11.6457 Evaluate side-chains 61 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 93 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.0470 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.0470 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.0170 chunk 21 optimal weight: 2.9990 overall best weight: 0.2814 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.226968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.184082 restraints weight = 3282.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.189284 restraints weight = 2097.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.192589 restraints weight = 1535.615| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2743 Z= 0.101 Angle : 0.446 5.026 3696 Z= 0.236 Chirality : 0.039 0.114 387 Planarity : 0.004 0.046 454 Dihedral : 8.580 53.336 443 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.63 % Allowed : 19.17 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.36 (0.49), residues: 323 helix: 2.80 (0.40), residues: 165 sheet: 0.29 (0.60), residues: 68 loop : 0.29 (0.74), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.002 0.000 HIS A 84 PHE 0.007 0.001 PHE C 68 TYR 0.011 0.001 TYR B 85 ARG 0.002 0.000 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 168) hydrogen bonds : angle 3.80844 ( 480) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.37957 ( 2) covalent geometry : bond 0.00210 ( 2742) covalent geometry : angle 0.44554 ( 3694) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: B 23 MET cc_start: 0.7956 (tpp) cc_final: 0.7332 (mmt) REVERT: B 62 ARG cc_start: 0.6940 (ttp-170) cc_final: 0.6716 (ttp-170) REVERT: A 72 LYS cc_start: 0.8048 (tptt) cc_final: 0.7358 (tptt) REVERT: A 103 MET cc_start: 0.4620 (ptm) cc_final: 0.4390 (ptm) REVERT: C 7 SER cc_start: 0.8773 (t) cc_final: 0.8508 (p) REVERT: C 32 ARG cc_start: 0.8614 (mmm-85) cc_final: 0.8391 (mmt-90) REVERT: C 52 ASP cc_start: 0.8411 (m-30) cc_final: 0.8124 (m-30) REVERT: C 60 TYR cc_start: 0.7564 (m-80) cc_final: 0.6737 (m-80) REVERT: C 105 LYS cc_start: 0.7647 (pttt) cc_final: 0.7190 (ptpp) outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 0.1729 time to fit residues: 12.2152 Evaluate side-chains 59 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 93 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 0.0000 chunk 21 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.222062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.178725 restraints weight = 3286.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.183751 restraints weight = 2143.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.187037 restraints weight = 1590.559| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2743 Z= 0.122 Angle : 0.488 7.138 3696 Z= 0.261 Chirality : 0.039 0.120 387 Planarity : 0.004 0.045 454 Dihedral : 8.773 58.349 443 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.26 % Allowed : 18.80 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.38 (0.49), residues: 323 helix: 2.78 (0.40), residues: 165 sheet: 0.30 (0.62), residues: 65 loop : 0.40 (0.73), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 50 HIS 0.003 0.001 HIS A 84 PHE 0.009 0.001 PHE B 112 TYR 0.013 0.001 TYR A 62 ARG 0.002 0.000 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 168) hydrogen bonds : angle 3.87480 ( 480) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.38115 ( 2) covalent geometry : bond 0.00269 ( 2742) covalent geometry : angle 0.48800 ( 3694) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.288 Fit side-chains REVERT: B 62 ARG cc_start: 0.7006 (ttp-170) cc_final: 0.6783 (ttp-170) REVERT: A 72 LYS cc_start: 0.8113 (tptt) cc_final: 0.7463 (tptt) REVERT: A 103 MET cc_start: 0.4686 (ptm) cc_final: 0.4434 (ptm) REVERT: C 7 SER cc_start: 0.8756 (t) cc_final: 0.8525 (p) REVERT: C 32 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8400 (mmt-90) REVERT: C 52 ASP cc_start: 0.8488 (m-30) cc_final: 0.8177 (m-30) REVERT: C 60 TYR cc_start: 0.7598 (m-80) cc_final: 0.6856 (m-80) outliers start: 6 outliers final: 6 residues processed: 60 average time/residue: 0.1715 time to fit residues: 12.1885 Evaluate side-chains 62 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 62 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 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 = 0.4345 r_free = 0.4345 target = 0.223061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.179987 restraints weight = 3290.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.184940 restraints weight = 2149.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.188053 restraints weight = 1601.846| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2743 Z= 0.126 Angle : 0.493 5.441 3696 Z= 0.267 Chirality : 0.039 0.125 387 Planarity : 0.004 0.046 454 Dihedral : 8.768 54.634 443 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.26 % Allowed : 19.55 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.28 (0.48), residues: 323 helix: 2.71 (0.40), residues: 165 sheet: 0.16 (0.62), residues: 65 loop : 0.40 (0.72), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 47 HIS 0.003 0.001 HIS A 84 PHE 0.006 0.001 PHE C 68 TYR 0.013 0.001 TYR A 62 ARG 0.003 0.000 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 168) hydrogen bonds : angle 3.98295 ( 480) SS BOND : bond 0.00146 ( 1) SS BOND : angle 0.38746 ( 2) covalent geometry : bond 0.00276 ( 2742) covalent geometry : angle 0.49265 ( 3694) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.307 Fit side-chains REVERT: B 62 ARG cc_start: 0.7030 (ttp-170) cc_final: 0.6813 (ttp-170) REVERT: A 72 LYS cc_start: 0.8100 (tptt) cc_final: 0.7469 (tptt) REVERT: A 103 MET cc_start: 0.4673 (ptm) cc_final: 0.4430 (ptm) REVERT: C 7 SER cc_start: 0.8759 (t) cc_final: 0.8521 (p) REVERT: C 32 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8417 (mmt-90) REVERT: C 52 ASP cc_start: 0.8486 (m-30) cc_final: 0.8073 (m-30) REVERT: C 60 TYR cc_start: 0.7553 (m-80) cc_final: 0.6850 (m-80) outliers start: 6 outliers final: 6 residues processed: 62 average time/residue: 0.1713 time to fit residues: 12.5759 Evaluate side-chains 62 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 62 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 12 optimal weight: 0.0970 chunk 29 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.222537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.180206 restraints weight = 3269.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.184441 restraints weight = 2125.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.188270 restraints weight = 1605.395| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2743 Z= 0.120 Angle : 0.479 6.523 3696 Z= 0.258 Chirality : 0.039 0.117 387 Planarity : 0.005 0.045 454 Dihedral : 8.583 48.463 443 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.26 % Allowed : 20.30 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.30 (0.49), residues: 323 helix: 2.72 (0.40), residues: 165 sheet: 0.13 (0.62), residues: 65 loop : 0.47 (0.73), residues: 93 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 0.007 0.001 PHE A 57 TYR 0.013 0.001 TYR A 62 ARG 0.002 0.000 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 168) hydrogen bonds : angle 3.90739 ( 480) SS BOND : bond 0.00159 ( 1) SS BOND : angle 0.45959 ( 2) covalent geometry : bond 0.00264 ( 2742) covalent geometry : angle 0.47912 ( 3694) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1823.91 seconds wall clock time: 32 minutes 15.68 seconds (1935.68 seconds total)