Starting phenix.real_space_refine on Fri May 9 14:46:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9knx_62465/05_2025/9knx_62465.cif Found real_map, /net/cci-nas-00/data/ceres_data/9knx_62465/05_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_62465/05_2025/9knx_62465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9knx_62465/05_2025/9knx_62465.map" model { file = "/net/cci-nas-00/data/ceres_data/9knx_62465/05_2025/9knx_62465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9knx_62465/05_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-5687/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: 2.70, per 1000 atoms: 1.01 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: 0.76 Conformation dependent library (CDL) restraints added in 356.5 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: 0.29 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: 0.72 Time building geometry restraints manager: 0.83 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: 1.330 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.570 ------------------------------------------------------------------------------- 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 : 0.276 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: 0.1671 time to fit residues: 11.7929 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 : 0.273 ------------------------------------------------------------------------------- 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 = 0.180580 restraints weight = 3310.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.186015 restraints weight = 2056.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.189128 restraints weight = 1500.602| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 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: 0.8488 (mttt) cc_final: 0.8279 (ttmm) REVERT: A 72 LYS cc_start: 0.7784 (tptt) cc_final: 0.7249 (tptt) REVERT: A 103 MET cc_start: 0.4469 (ptm) cc_final: 0.4257 (ptm) REVERT: C 60 TYR cc_start: 0.7973 (m-80) cc_final: 0.7288 (m-80) outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.1671 time to fit residues: 9.7350 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 : 0.295 ------------------------------------------------------------------------------- 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: 0.3980 chunk 2 optimal weight: 0.0770 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.0570 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 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 = 0.4381 r_free = 0.4381 target = 0.228102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.184904 restraints weight = 3229.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.189681 restraints weight = 2099.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.193229 restraints weight = 1577.541| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2743 Z= 0.115 Angle : 0.485 7.591 3696 Z= 0.255 Chirality : 0.039 0.144 387 Planarity : 0.004 0.047 454 Dihedral : 11.556 59.015 443 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: 1.33 (0.48), residues: 323 helix: 1.80 (0.41), residues: 165 sheet: 0.27 (0.58), residues: 68 loop : -0.23 (0.71), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 44 HIS 0.002 0.001 HIS A 84 PHE 0.008 0.001 PHE A 57 TYR 0.013 0.001 TYR B 85 ARG 0.002 0.000 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 168) hydrogen bonds : angle 4.31480 ( 480) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.33947 ( 2) covalent geometry : bond 0.00242 ( 2742) covalent geometry : angle 0.48541 ( 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 54 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 LYS cc_start: 0.8538 (mttt) cc_final: 0.8302 (ttmm) REVERT: B 62 ARG cc_start: 0.7150 (ttt180) cc_final: 0.6834 (ttp-170) REVERT: A 72 LYS cc_start: 0.7898 (tptt) cc_final: 0.7148 (tptt) REVERT: A 103 MET cc_start: 0.4508 (ptm) cc_final: 0.4264 (ptm) REVERT: C 60 TYR cc_start: 0.7876 (m-80) cc_final: 0.7304 (m-80) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 0.1771 time to fit residues: 11.0359 Evaluate side-chains 50 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 2 optimal weight: 0.0770 chunk 14 optimal weight: 0.0030 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.5150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 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 = 0.4341 r_free = 0.4341 target = 0.224016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.178485 restraints weight = 3268.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.183801 restraints weight = 2071.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.187682 restraints weight = 1520.429| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2743 Z= 0.112 Angle : 0.492 8.997 3696 Z= 0.250 Chirality : 0.040 0.185 387 Planarity : 0.004 0.047 454 Dihedral : 10.003 53.723 443 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.26 % Allowed : 14.29 % Favored : 83.46 % 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: 1.82 (0.48), residues: 323 helix: 2.31 (0.41), residues: 165 sheet: 0.40 (0.58), residues: 68 loop : -0.18 (0.72), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 82 HIS 0.003 0.001 HIS A 84 PHE 0.006 0.001 PHE A 57 TYR 0.012 0.001 TYR B 85 ARG 0.002 0.000 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 168) hydrogen bonds : angle 3.99624 ( 480) SS BOND : bond 0.00196 ( 1) SS BOND : angle 0.15398 ( 2) covalent geometry : bond 0.00240 ( 2742) covalent geometry : angle 0.49187 ( 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 59 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 MET cc_start: 0.7748 (mmt) cc_final: 0.7285 (mmt) REVERT: B 27 LYS cc_start: 0.8544 (mttt) cc_final: 0.8315 (ttmm) REVERT: A 103 MET cc_start: 0.4507 (ptm) cc_final: 0.4250 (ptm) REVERT: C 60 TYR cc_start: 0.7889 (m-80) cc_final: 0.7233 (m-80) outliers start: 6 outliers final: 4 residues processed: 57 average time/residue: 0.1693 time to fit residues: 11.3630 Evaluate side-chains 56 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.210061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.165592 restraints weight = 3153.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.170301 restraints weight = 2003.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.174061 restraints weight = 1466.606| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3460 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= 0.147 Angle : 0.515 6.450 3696 Z= 0.270 Chirality : 0.040 0.155 387 Planarity : 0.004 0.047 454 Dihedral : 9.942 56.455 443 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.63 % Allowed : 18.42 % 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: 1.93 (0.48), residues: 323 helix: 2.35 (0.40), residues: 165 sheet: 0.53 (0.64), residues: 61 loop : -0.05 (0.69), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS A 84 PHE 0.009 0.002 PHE A 57 TYR 0.014 0.001 TYR B 85 ARG 0.002 0.000 ARG C 67 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 168) hydrogen bonds : angle 4.09974 ( 480) SS BOND : bond 0.00100 ( 1) SS BOND : angle 0.31433 ( 2) covalent geometry : bond 0.00331 ( 2742) covalent geometry : angle 0.51559 ( 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 58 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 MET cc_start: 0.7769 (mmt) cc_final: 0.6799 (mpp) REVERT: B 27 LYS cc_start: 0.8530 (mttt) cc_final: 0.8274 (ttmm) REVERT: B 62 ARG cc_start: 0.7136 (ttp-170) cc_final: 0.6848 (ttp-170) REVERT: A 103 MET cc_start: 0.4755 (ptm) cc_final: 0.4471 (ptm) REVERT: C 60 TYR cc_start: 0.7858 (m-80) cc_final: 0.7287 (m-80) REVERT: C 83 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7507 (tpp) outliers start: 7 outliers final: 6 residues processed: 55 average time/residue: 0.1713 time to fit residues: 11.0898 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 : 0.282 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 83 MET 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: 1.9990 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 0.0060 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.223586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.179404 restraints weight = 3302.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.184818 restraints weight = 2086.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.188496 restraints weight = 1522.627| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2743 Z= 0.116 Angle : 0.479 5.994 3696 Z= 0.249 Chirality : 0.039 0.154 387 Planarity : 0.004 0.047 454 Dihedral : 9.358 53.690 443 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.63 % Allowed : 18.05 % Favored : 79.32 % 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: 1.94 (0.48), residues: 323 helix: 2.48 (0.40), residues: 165 sheet: 0.15 (0.60), residues: 65 loop : 0.02 (0.72), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 50 HIS 0.003 0.000 HIS A 84 PHE 0.007 0.001 PHE A 57 TYR 0.012 0.001 TYR B 85 ARG 0.002 0.000 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 168) hydrogen bonds : angle 3.92844 ( 480) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.24070 ( 2) covalent geometry : bond 0.00251 ( 2742) covalent geometry : angle 0.47870 ( 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: 7 poor density : 51 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 LYS cc_start: 0.8527 (mttt) cc_final: 0.8318 (ttmm) REVERT: B 62 ARG cc_start: 0.7107 (ttp-170) cc_final: 0.6844 (ttp-170) REVERT: A 103 MET cc_start: 0.4664 (ptm) cc_final: 0.4443 (ptm) REVERT: C 32 ARG cc_start: 0.8595 (mmm-85) cc_final: 0.8252 (mmt-90) REVERT: C 52 ASP cc_start: 0.8536 (m-30) cc_final: 0.8328 (m-30) REVERT: C 60 TYR cc_start: 0.7725 (m-80) cc_final: 0.7133 (m-80) outliers start: 7 outliers final: 6 residues processed: 55 average time/residue: 0.1695 time to fit residues: 11.0040 Evaluate side-chains 57 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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: 0.0060 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 30.0000 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 0.1980 overall best weight: 0.3294 ------------------------------------------------------------------------------- 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 = 0.4358 r_free = 0.4358 target = 0.225011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.182411 restraints weight = 3307.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.187806 restraints weight = 2021.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.191672 restraints weight = 1441.269| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2743 Z= 0.103 Angle : 0.469 5.944 3696 Z= 0.243 Chirality : 0.039 0.115 387 Planarity : 0.004 0.046 454 Dihedral : 8.805 51.121 443 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.63 % Allowed : 18.05 % Favored : 79.32 % 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: 2.19 (0.48), residues: 323 helix: 2.70 (0.40), residues: 165 sheet: 0.14 (0.60), residues: 65 loop : 0.20 (0.72), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 34 HIS 0.002 0.000 HIS A 84 PHE 0.008 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 0.04100 ( 168) hydrogen bonds : angle 3.85327 ( 480) SS BOND : bond 0.00183 ( 1) SS BOND : angle 0.31171 ( 2) covalent geometry : bond 0.00216 ( 2742) covalent geometry : angle 0.46910 ( 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 59 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 62 ARG cc_start: 0.6949 (ttp-170) cc_final: 0.6731 (ttp-170) REVERT: A 103 MET cc_start: 0.4743 (ptm) cc_final: 0.4509 (ptm) REVERT: C 32 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.8259 (mmt-90) REVERT: C 60 TYR cc_start: 0.7694 (m-80) cc_final: 0.7065 (m-80) outliers start: 7 outliers final: 5 residues processed: 55 average time/residue: 0.1717 time to fit residues: 11.1275 Evaluate side-chains 54 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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: 0.0770 chunk 24 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 overall best weight: 0.1916 ------------------------------------------------------------------------------- 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 = 0.4401 r_free = 0.4401 target = 0.229389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.186231 restraints weight = 3257.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.191600 restraints weight = 2041.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.195374 restraints weight = 1482.620| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.4315 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= 0.102 Angle : 0.470 5.912 3696 Z= 0.250 Chirality : 0.038 0.114 387 Planarity : 0.004 0.046 454 Dihedral : 8.303 49.904 443 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.26 % Allowed : 19.92 % Favored : 77.82 % 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: 2.40 (0.49), residues: 323 helix: 2.79 (0.40), residues: 167 sheet: 0.33 (0.60), residues: 68 loop : 0.34 (0.75), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 82 HIS 0.002 0.000 HIS A 84 PHE 0.012 0.001 PHE C 68 TYR 0.010 0.001 TYR B 85 ARG 0.002 0.000 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 168) hydrogen bonds : angle 3.75046 ( 480) SS BOND : bond 0.00204 ( 1) SS BOND : angle 0.33474 ( 2) covalent geometry : bond 0.00210 ( 2742) covalent geometry : angle 0.47050 ( 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 56 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.279 Fit side-chains REVERT: A 72 LYS cc_start: 0.7989 (tptt) cc_final: 0.7280 (tptt) REVERT: A 103 MET cc_start: 0.4618 (ptm) cc_final: 0.4388 (ptm) REVERT: C 52 ASP cc_start: 0.8356 (m-30) cc_final: 0.8126 (m-30) REVERT: C 60 TYR cc_start: 0.7626 (m-80) cc_final: 0.6905 (m-80) REVERT: C 105 LYS cc_start: 0.7648 (pttt) cc_final: 0.7174 (ptpp) outliers start: 6 outliers final: 6 residues processed: 55 average time/residue: 0.1649 time to fit residues: 10.7354 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 : 0.278 ------------------------------------------------------------------------------- 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: 5.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 21 optimal weight: 20.0000 chunk 8 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.227603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.184333 restraints weight = 3287.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.189380 restraints weight = 2136.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.192201 restraints weight = 1593.482| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2743 Z= 0.112 Angle : 0.468 5.132 3696 Z= 0.253 Chirality : 0.039 0.113 387 Planarity : 0.004 0.045 454 Dihedral : 8.354 50.243 443 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: 2.47 (0.49), residues: 323 helix: 2.85 (0.40), residues: 167 sheet: 0.37 (0.60), residues: 68 loop : 0.34 (0.75), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 50 HIS 0.002 0.001 HIS A 84 PHE 0.012 0.001 PHE C 68 TYR 0.012 0.001 TYR B 85 ARG 0.001 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 168) hydrogen bonds : angle 3.78299 ( 480) SS BOND : bond 0.00144 ( 1) SS BOND : angle 0.38540 ( 2) covalent geometry : bond 0.00241 ( 2742) covalent geometry : angle 0.46814 ( 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 54 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.300 Fit side-chains REVERT: A 72 LYS cc_start: 0.8081 (tptt) cc_final: 0.7383 (tptt) REVERT: A 103 MET cc_start: 0.4559 (ptm) cc_final: 0.4326 (ptm) REVERT: C 52 ASP cc_start: 0.8313 (m-30) cc_final: 0.8069 (m-30) REVERT: C 60 TYR cc_start: 0.7641 (m-80) cc_final: 0.6948 (m-80) REVERT: C 105 LYS cc_start: 0.7667 (pttt) cc_final: 0.7200 (ptpp) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.1758 time to fit residues: 11.2689 Evaluate side-chains 53 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.0020 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.226639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.183553 restraints weight = 3291.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.188717 restraints weight = 2129.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.192120 restraints weight = 1578.971| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2743 Z= 0.110 Angle : 0.474 6.834 3696 Z= 0.252 Chirality : 0.039 0.119 387 Planarity : 0.004 0.045 454 Dihedral : 8.329 50.380 443 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.88 % Allowed : 19.55 % Favored : 78.57 % 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: 2.52 (0.49), residues: 323 helix: 2.81 (0.39), residues: 168 sheet: 0.42 (0.61), residues: 68 loop : 0.51 (0.76), residues: 87 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 0.010 0.001 PHE C 68 TYR 0.011 0.001 TYR B 85 ARG 0.001 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 168) hydrogen bonds : angle 3.73416 ( 480) SS BOND : bond 0.00195 ( 1) SS BOND : angle 0.44044 ( 2) covalent geometry : bond 0.00240 ( 2742) covalent geometry : angle 0.47424 ( 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 53 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.301 Fit side-chains REVERT: A 72 LYS cc_start: 0.8064 (tptt) cc_final: 0.7267 (tttt) REVERT: A 103 MET cc_start: 0.4601 (ptm) cc_final: 0.4350 (ptm) REVERT: C 52 ASP cc_start: 0.8350 (m-30) cc_final: 0.8125 (m-30) REVERT: C 60 TYR cc_start: 0.7582 (m-80) cc_final: 0.6906 (m-80) REVERT: C 105 LYS cc_start: 0.7706 (pttt) cc_final: 0.7257 (ptpp) outliers start: 5 outliers final: 5 residues processed: 53 average time/residue: 0.1426 time to fit residues: 9.1140 Evaluate side-chains 53 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.0270 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.225632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.182459 restraints weight = 3266.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.187479 restraints weight = 2110.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.191124 restraints weight = 1562.483| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2743 Z= 0.116 Angle : 0.482 5.247 3696 Z= 0.260 Chirality : 0.039 0.115 387 Planarity : 0.004 0.045 454 Dihedral : 8.446 51.680 443 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.88 % Allowed : 19.55 % Favored : 78.57 % 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: 2.52 (0.49), residues: 323 helix: 2.84 (0.40), residues: 167 sheet: 0.44 (0.61), residues: 68 loop : 0.44 (0.76), residues: 88 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 0.010 0.001 PHE C 68 TYR 0.012 0.001 TYR B 85 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 168) hydrogen bonds : angle 3.79944 ( 480) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.44999 ( 2) covalent geometry : bond 0.00253 ( 2742) covalent geometry : angle 0.48207 ( 3694) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1685.56 seconds wall clock time: 30 minutes 22.77 seconds (1822.77 seconds total)