Starting phenix.real_space_refine on Sat Apr 26 14:57:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hvc_52431/04_2025/9hvc_52431.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hvc_52431/04_2025/9hvc_52431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hvc_52431/04_2025/9hvc_52431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hvc_52431/04_2025/9hvc_52431.map" model { file = "/net/cci-nas-00/data/ceres_data/9hvc_52431/04_2025/9hvc_52431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hvc_52431/04_2025/9hvc_52431.cif" } resolution = 2.24 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= 0.003 sd= 0.055 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 1 5.49 5 S 6 5.16 5 C 363 2.51 5 N 75 2.21 5 O 133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 578 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 498 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 80 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1, 'water': 31} Link IDs: {None: 31} Time building chain proxies: 1.72, per 1000 atoms: 2.98 Number of scatterers: 578 At special positions: 0 Unit cell: (38.76, 53.04, 58.14, 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 6 16.00 P 1 15.00 O 133 8.00 N 75 7.00 C 363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Links applied TRANS " GLY A 1 " - " ASP A 69 " Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 176.7 milliseconds 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 120 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 removed outlier: 4.104A pdb=" N THR A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 44 through 59 Processing helix chain 'A' and resid 59 through 68 42 hydrogen bonds defined for protein. 126 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: 0.10 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 100 1.33 - 1.45: 121 1.45 - 1.57: 321 1.57 - 1.69: 2 1.69 - 1.80: 11 Bond restraints: 555 Sorted by residual: bond pdb=" C23 LHG A 101 " pdb=" O8 LHG A 101 " ideal model delta sigma weight residual 1.328 1.366 -0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb=" C7 LHG A 101 " pdb=" O7 LHG A 101 " ideal model delta sigma weight residual 1.329 1.362 -0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" C7 LHG A 101 " pdb=" C8 LHG A 101 " ideal model delta sigma weight residual 1.507 1.476 0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C20 LHG A 101 " pdb=" C21 LHG A 101 " ideal model delta sigma weight residual 1.527 1.497 0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C36 LHG A 101 " pdb=" C37 LHG A 101 " ideal model delta sigma weight residual 1.526 1.497 0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 702 2.49 - 4.99: 16 4.99 - 7.48: 9 7.48 - 9.97: 6 9.97 - 12.46: 5 Bond angle restraints: 738 Sorted by residual: angle pdb=" O4 LHG A 101 " pdb=" P LHG A 101 " pdb=" O5 LHG A 101 " ideal model delta sigma weight residual 120.69 133.15 -12.46 3.00e+00 1.11e-01 1.73e+01 angle pdb=" C2 LHG A 101 " pdb=" C3 LHG A 101 " pdb=" O3 LHG A 101 " ideal model delta sigma weight residual 111.30 99.73 11.57 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C11 LHG A 101 " pdb=" C10 LHG A 101 " pdb=" C9 LHG A 101 " ideal model delta sigma weight residual 112.80 101.96 10.84 3.00e+00 1.11e-01 1.31e+01 angle pdb=" C18 LHG A 101 " pdb=" C19 LHG A 101 " pdb=" C20 LHG A 101 " ideal model delta sigma weight residual 113.04 102.58 10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C16 LHG A 101 " pdb=" C17 LHG A 101 " pdb=" C18 LHG A 101 " ideal model delta sigma weight residual 113.58 103.50 10.08 3.00e+00 1.11e-01 1.13e+01 ... (remaining 733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.39: 262 14.39 - 28.77: 48 28.77 - 43.16: 18 43.16 - 57.55: 10 57.55 - 71.93: 4 Dihedral angle restraints: 342 sinusoidal: 151 harmonic: 191 Sorted by residual: dihedral pdb=" CA GLY A 1 " pdb=" N GLY A 1 " pdb=" C ASP A 69 " pdb=" CA ASP A 69 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ASN A 43 " pdb=" CB ASN A 43 " pdb=" CG ASN A 43 " pdb=" OD1 ASN A 43 " ideal model delta sinusoidal sigma weight residual -90.00 -161.93 71.93 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CB LYS A 41 " pdb=" CG LYS A 41 " pdb=" CD LYS A 41 " pdb=" CE LYS A 41 " ideal model delta sinusoidal sigma weight residual 60.00 118.06 -58.06 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 339 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.019: 37 0.019 - 0.037: 22 0.037 - 0.055: 4 0.055 - 0.073: 14 0.073 - 0.091: 4 Chirality restraints: 81 Sorted by residual: chirality pdb=" CA PRO A 22 " pdb=" N PRO A 22 " pdb=" C PRO A 22 " pdb=" CB PRO A 22 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.09 2.00e-01 2.50e+01 2.08e-01 chirality pdb=" C5 LHG A 101 " pdb=" C4 LHG A 101 " pdb=" C6 LHG A 101 " pdb=" O7 LHG A 101 " both_signs ideal model delta sigma weight residual False -2.53 -2.62 0.09 2.00e-01 2.50e+01 2.01e-01 chirality pdb=" CA ASN A 43 " pdb=" N ASN A 43 " pdb=" C ASN A 43 " pdb=" CB ASN A 43 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.64e-01 ... (remaining 78 not shown) Planarity restraints: 88 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 LHG A 101 " -0.066 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C8 LHG A 101 " 0.019 2.00e-02 2.50e+03 pdb=" O7 LHG A 101 " 0.020 2.00e-02 2.50e+03 pdb=" O9 LHG A 101 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 43 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" CG ASN A 43 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 43 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 43 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 LHG A 101 " 0.025 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C24 LHG A 101 " -0.008 2.00e-02 2.50e+03 pdb=" O10 LHG A 101 " -0.009 2.00e-02 2.50e+03 pdb=" O8 LHG A 101 " -0.008 2.00e-02 2.50e+03 ... (remaining 85 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 21 2.73 - 3.27: 581 3.27 - 3.81: 936 3.81 - 4.36: 1069 4.36 - 4.90: 1652 Nonbonded interactions: 4259 Sorted by model distance: nonbonded pdb=" O2 LHG A 101 " pdb=" O3 LHG A 101 " model vdw 2.184 2.432 nonbonded pdb=" O ASP A 69 " pdb=" O HOH A 201 " model vdw 2.269 3.040 nonbonded pdb=" O HOH A 206 " pdb=" O HOH A 218 " model vdw 2.283 3.040 nonbonded pdb=" O6 LHG A 101 " pdb=" O7 LHG A 101 " model vdw 2.307 2.432 nonbonded pdb=" O HOH A 230 " pdb=" O HOH A 231 " model vdw 2.309 3.040 ... (remaining 4254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.450 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.660 Find NCS groups from input model: 0.000 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:10.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5732 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 : 0.006 0.038 556 Z= 0.285 Angle : 1.608 12.463 741 Z= 0.599 Chirality : 0.037 0.091 81 Planarity : 0.005 0.038 87 Dihedral : 19.496 71.933 219 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.75 (0.99), residues: 67 helix: 2.47 (0.64), residues: 57 sheet: None (None), residues: 0 loop : -2.33 (1.71), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 11 PHE 0.005 0.001 PHE A 37 TYR 0.007 0.002 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00093 ( 1) link_TRANS : angle 7.19268 ( 3) hydrogen bonds : bond 0.15986 ( 42) hydrogen bonds : angle 5.38301 ( 126) covalent geometry : bond 0.00583 ( 555) covalent geometry : angle 1.54436 ( 738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.042 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.8448 time to fit residues: 10.2577 Evaluate side-chains 10 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 overall best weight: 1.8987 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.124462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110761 restraints weight = 578.824| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.33 r_work: 0.3224 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 1.0100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 556 Z= 0.193 Angle : 0.571 3.690 741 Z= 0.290 Chirality : 0.041 0.108 81 Planarity : 0.004 0.025 87 Dihedral : 17.005 58.938 115 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.92 % Allowed : 17.65 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.14 (0.98), residues: 67 helix: 2.71 (0.63), residues: 57 sheet: None (None), residues: 0 loop : -2.00 (1.84), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 11 PHE 0.006 0.001 PHE A 7 TYR 0.010 0.002 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00084 ( 1) link_TRANS : angle 0.52114 ( 3) hydrogen bonds : bond 0.04082 ( 42) hydrogen bonds : angle 4.31252 ( 126) covalent geometry : bond 0.00381 ( 555) covalent geometry : angle 0.57169 ( 738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.059 Fit side-chains REVERT: A 53 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8086 (tpt) outliers start: 2 outliers final: 0 residues processed: 12 average time/residue: 1.3271 time to fit residues: 16.0823 Evaluate side-chains 11 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** 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 = 0.3451 r_free = 0.3451 target = 0.118276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105264 restraints weight = 583.121| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.28 r_work: 0.3163 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 1.0386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 556 Z= 0.147 Angle : 0.430 4.573 741 Z= 0.218 Chirality : 0.037 0.088 81 Planarity : 0.004 0.025 87 Dihedral : 14.744 55.015 115 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.96 % Allowed : 21.57 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.10 (1.00), residues: 67 helix: 2.65 (0.64), residues: 57 sheet: None (None), residues: 0 loop : -1.80 (1.90), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 11 PHE 0.010 0.001 PHE A 7 TYR 0.011 0.002 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00098 ( 1) link_TRANS : angle 0.53779 ( 3) hydrogen bonds : bond 0.04011 ( 42) hydrogen bonds : angle 4.25164 ( 126) covalent geometry : bond 0.00312 ( 555) covalent geometry : angle 0.42966 ( 738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.056 Fit side-chains REVERT: A 53 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8135 (tpt) outliers start: 1 outliers final: 0 residues processed: 12 average time/residue: 1.3793 time to fit residues: 16.7046 Evaluate side-chains 13 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5313 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112205 restraints weight = 555.892| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.21 r_work: 0.3267 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 1.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 556 Z= 0.076 Angle : 0.333 4.640 741 Z= 0.166 Chirality : 0.032 0.092 81 Planarity : 0.003 0.023 87 Dihedral : 12.464 49.944 115 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 13.73 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.64 (1.00), residues: 67 helix: 3.08 (0.65), residues: 57 sheet: None (None), residues: 0 loop : -2.04 (1.70), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 11 PHE 0.003 0.001 PHE A 7 TYR 0.004 0.001 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00042 ( 1) link_TRANS : angle 0.26943 ( 3) hydrogen bonds : bond 0.02592 ( 42) hydrogen bonds : angle 3.88343 ( 126) covalent geometry : bond 0.00138 ( 555) covalent geometry : angle 0.33349 ( 738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.061 Fit side-chains REVERT: A 16 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7899 (mt-10) REVERT: A 53 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8200 (tpt) outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 1.3130 time to fit residues: 18.5520 Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8983 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107969 restraints weight = 588.612| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.25 r_work: 0.3190 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 1.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 556 Z= 0.094 Angle : 0.355 4.626 741 Z= 0.182 Chirality : 0.034 0.090 81 Planarity : 0.003 0.023 87 Dihedral : 12.781 53.183 115 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 11.76 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.81 (1.01), residues: 67 helix: 3.21 (0.66), residues: 57 sheet: None (None), residues: 0 loop : -2.09 (1.65), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 11 PHE 0.005 0.001 PHE A 7 TYR 0.005 0.001 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00073 ( 1) link_TRANS : angle 0.18556 ( 3) hydrogen bonds : bond 0.02996 ( 42) hydrogen bonds : angle 3.95565 ( 126) covalent geometry : bond 0.00181 ( 555) covalent geometry : angle 0.35505 ( 738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.058 Fit side-chains REVERT: A 16 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7866 (mt-10) REVERT: A 53 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8078 (tpt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 1.2050 time to fit residues: 15.8274 Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 overall best weight: 2.2987 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.116883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104632 restraints weight = 595.182| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.28 r_work: 0.3133 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 1.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 556 Z= 0.159 Angle : 0.427 4.779 741 Z= 0.211 Chirality : 0.036 0.088 81 Planarity : 0.003 0.022 87 Dihedral : 14.184 57.988 115 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 13.73 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.65 (1.00), residues: 67 helix: 3.07 (0.66), residues: 57 sheet: None (None), residues: 0 loop : -1.96 (1.64), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 11 PHE 0.007 0.002 PHE A 7 TYR 0.011 0.003 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00293 ( 1) link_TRANS : angle 0.14318 ( 3) hydrogen bonds : bond 0.03799 ( 42) hydrogen bonds : angle 4.22915 ( 126) covalent geometry : bond 0.00345 ( 555) covalent geometry : angle 0.42820 ( 738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.060 Fit side-chains REVERT: A 16 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7958 (mt-10) REVERT: A 43 ASN cc_start: 0.7920 (t0) cc_final: 0.7654 (t0) REVERT: A 53 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8036 (tpt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 1.3617 time to fit residues: 17.8588 Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 overall best weight: 1.2653 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** 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 = 0.3448 r_free = 0.3448 target = 0.118885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107062 restraints weight = 577.559| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.24 r_work: 0.3175 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 1.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 556 Z= 0.105 Angle : 0.367 4.779 741 Z= 0.184 Chirality : 0.034 0.088 81 Planarity : 0.003 0.022 87 Dihedral : 13.097 50.840 115 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 13.73 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.96 (1.01), residues: 67 helix: 3.30 (0.66), residues: 57 sheet: None (None), residues: 0 loop : -1.95 (1.49), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 11 PHE 0.004 0.001 PHE A 7 TYR 0.008 0.002 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00107 ( 1) link_TRANS : angle 0.12034 ( 3) hydrogen bonds : bond 0.03155 ( 42) hydrogen bonds : angle 4.02931 ( 126) covalent geometry : bond 0.00214 ( 555) covalent geometry : angle 0.36784 ( 738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.064 Fit side-chains REVERT: A 16 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7916 (mt-10) REVERT: A 43 ASN cc_start: 0.7885 (t0) cc_final: 0.7630 (t0) REVERT: A 53 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8037 (tpt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 1.2615 time to fit residues: 16.5705 Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 1.1650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** 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 = 0.3460 r_free = 0.3460 target = 0.119475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.107340 restraints weight = 616.247| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.31 r_work: 0.3176 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 1.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 556 Z= 0.101 Angle : 0.373 4.795 741 Z= 0.184 Chirality : 0.034 0.088 81 Planarity : 0.003 0.021 87 Dihedral : 12.705 46.291 115 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 13.73 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.97 (1.00), residues: 67 helix: 3.28 (0.66), residues: 57 sheet: None (None), residues: 0 loop : -1.80 (1.40), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 11 PHE 0.005 0.001 PHE A 7 TYR 0.006 0.002 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00120 ( 1) link_TRANS : angle 0.08239 ( 3) hydrogen bonds : bond 0.03125 ( 42) hydrogen bonds : angle 4.00831 ( 126) covalent geometry : bond 0.00203 ( 555) covalent geometry : angle 0.37329 ( 738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.061 Fit side-chains REVERT: A 16 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7843 (mt-10) REVERT: A 43 ASN cc_start: 0.7864 (t0) cc_final: 0.7633 (t0) REVERT: A 53 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8063 (tpt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 1.2575 time to fit residues: 16.5070 Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 1.9987 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.117466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105469 restraints weight = 583.103| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.27 r_work: 0.3148 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 1.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 556 Z= 0.141 Angle : 0.415 4.764 741 Z= 0.206 Chirality : 0.035 0.089 81 Planarity : 0.003 0.021 87 Dihedral : 13.150 49.447 115 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 13.73 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.76 (0.99), residues: 67 helix: 3.10 (0.66), residues: 57 sheet: None (None), residues: 0 loop : -1.55 (1.45), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 11 PHE 0.007 0.001 PHE A 7 TYR 0.009 0.002 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00266 ( 1) link_TRANS : angle 0.11304 ( 3) hydrogen bonds : bond 0.03566 ( 42) hydrogen bonds : angle 4.16728 ( 126) covalent geometry : bond 0.00300 ( 555) covalent geometry : angle 0.41590 ( 738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.062 Fit side-chains REVERT: A 16 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7942 (mt-10) REVERT: A 43 ASN cc_start: 0.7912 (t0) cc_final: 0.7617 (t0) REVERT: A 53 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8023 (tpt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 1.2203 time to fit residues: 16.0294 Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.0060 chunk 5 optimal weight: 6.9990 overall best weight: 0.9677 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** 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 = 0.3471 r_free = 0.3471 target = 0.120242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.108475 restraints weight = 584.960| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.26 r_work: 0.3194 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 1.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 556 Z= 0.093 Angle : 0.369 4.763 741 Z= 0.183 Chirality : 0.033 0.089 81 Planarity : 0.003 0.021 87 Dihedral : 12.685 49.022 115 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 13.73 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.10 (1.00), residues: 67 helix: 3.33 (0.66), residues: 57 sheet: None (None), residues: 0 loop : -1.47 (1.42), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 11 PHE 0.004 0.001 PHE A 7 TYR 0.007 0.001 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00100 ( 1) link_TRANS : angle 0.08615 ( 3) hydrogen bonds : bond 0.02957 ( 42) hydrogen bonds : angle 3.99198 ( 126) covalent geometry : bond 0.00180 ( 555) covalent geometry : angle 0.37015 ( 738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.061 Fit side-chains REVERT: A 16 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7895 (mt-10) REVERT: A 43 ASN cc_start: 0.7833 (t0) cc_final: 0.7620 (t160) REVERT: A 53 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8042 (tpt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 1.1944 time to fit residues: 15.6919 Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.118201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105835 restraints weight = 582.248| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.28 r_work: 0.3149 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 1.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 556 Z= 0.141 Angle : 0.422 4.780 741 Z= 0.209 Chirality : 0.036 0.089 81 Planarity : 0.003 0.021 87 Dihedral : 13.111 50.653 115 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.96 % Allowed : 15.69 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.89 (1.00), residues: 67 helix: 3.15 (0.66), residues: 57 sheet: None (None), residues: 0 loop : -1.26 (1.51), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 11 PHE 0.006 0.001 PHE A 7 TYR 0.010 0.003 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00284 ( 1) link_TRANS : angle 0.09607 ( 3) hydrogen bonds : bond 0.03538 ( 42) hydrogen bonds : angle 4.14119 ( 126) covalent geometry : bond 0.00301 ( 555) covalent geometry : angle 0.42298 ( 738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 881.27 seconds wall clock time: 16 minutes 37.92 seconds (997.92 seconds total)