Starting phenix.real_space_refine on Fri May 9 12:42:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hvc_52431/05_2025/9hvc_52431.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hvc_52431/05_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_52431/05_2025/9hvc_52431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hvc_52431/05_2025/9hvc_52431.map" model { file = "/net/cci-nas-00/data/ceres_data/9hvc_52431/05_2025/9hvc_52431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hvc_52431/05_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 1.76, per 1000 atoms: 3.04 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: 0.24 Conformation dependent library (CDL) restraints added in 68.7 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: 0.07 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: 0.13 Time building geometry restraints manager: 0.22 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: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 9.410 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.010 ------------------------------------------------------------------------------- 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 : 0.060 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 1.1394 time to fit residues: 13.8418 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 : 0.059 ------------------------------------------------------------------------------- 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: 0.0000 chunk 5 optimal weight: 3.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.136445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123273 restraints weight = 605.137| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.30 r_work: 0.3393 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.8906 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= 0.146 Angle : 0.579 4.445 741 Z= 0.259 Chirality : 0.036 0.093 81 Planarity : 0.004 0.025 87 Dihedral : 16.743 57.321 115 Min Nonbonded Distance : 2.683 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.92 % Allowed : 15.69 % Favored : 80.39 % 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: 3.15 (0.94), residues: 67 helix: 2.73 (0.60), residues: 57 sheet: None (None), residues: 0 loop : -2.06 (1.78), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 11 PHE 0.004 0.001 PHE A 37 TYR 0.010 0.002 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00069 ( 1) link_TRANS : angle 0.57431 ( 3) hydrogen bonds : bond 0.02599 ( 42) hydrogen bonds : angle 3.99011 ( 126) covalent geometry : bond 0.00281 ( 555) covalent geometry : angle 0.57941 ( 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 : 0.064 Fit side-chains REVERT: A 53 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7995 (tpt) outliers start: 2 outliers final: 0 residues processed: 12 average time/residue: 1.3857 time to fit residues: 16.7965 Evaluate side-chains 10 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.048 ------------------------------------------------------------------------------- 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: 0.8980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.9650 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.123991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.110731 restraints weight = 560.553| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.28 r_work: 0.3228 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.9975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 556 Z= 0.108 Angle : 0.367 4.531 741 Z= 0.190 Chirality : 0.035 0.087 81 Planarity : 0.003 0.025 87 Dihedral : 13.299 49.959 115 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: 3.74 (1.01), residues: 67 helix: 3.15 (0.65), residues: 57 sheet: None (None), residues: 0 loop : -2.07 (1.82), 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 0.006 0.002 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00022 ( 1) link_TRANS : angle 0.47717 ( 3) hydrogen bonds : bond 0.03483 ( 42) hydrogen bonds : angle 4.00894 ( 126) covalent geometry : bond 0.00211 ( 555) covalent geometry : angle 0.36635 ( 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 : 0.063 Fit side-chains REVERT: A 53 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8084 (tpt) outliers start: 1 outliers final: 0 residues processed: 12 average time/residue: 1.3480 time to fit residues: 16.3370 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 : 0.062 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7647 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.125280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112465 restraints weight = 552.625| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.23 r_work: 0.3257 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 1.0353 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= 0.083 Angle : 0.331 4.587 741 Z= 0.168 Chirality : 0.033 0.090 81 Planarity : 0.003 0.023 87 Dihedral : 12.432 52.051 115 Min Nonbonded Distance : 2.647 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: 4.02 (1.00), residues: 67 helix: 3.35 (0.64), residues: 57 sheet: None (None), residues: 0 loop : -2.05 (1.72), 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 0.004 0.001 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00052 ( 1) link_TRANS : angle 0.25603 ( 3) hydrogen bonds : bond 0.02727 ( 42) hydrogen bonds : angle 3.75297 ( 126) covalent geometry : bond 0.00159 ( 555) covalent geometry : angle 0.33158 ( 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 13 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.063 Fit side-chains REVERT: A 53 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8146 (tpt) outliers start: 1 outliers final: 0 residues processed: 12 average time/residue: 1.3382 time to fit residues: 16.2134 Evaluate side-chains 12 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.060 ------------------------------------------------------------------------------- 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: 0.9980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.123124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110279 restraints weight = 573.259| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.30 r_work: 0.3230 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 1.0483 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= 0.088 Angle : 0.332 4.687 741 Z= 0.172 Chirality : 0.034 0.089 81 Planarity : 0.003 0.022 87 Dihedral : 12.625 50.385 115 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 5.34 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: 4.18 (1.01), residues: 67 helix: 3.48 (0.65), residues: 57 sheet: None (None), residues: 0 loop : -2.09 (1.67), 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 0.006 0.001 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00030 ( 1) link_TRANS : angle 0.36206 ( 3) hydrogen bonds : bond 0.02827 ( 42) hydrogen bonds : angle 3.79260 ( 126) covalent geometry : bond 0.00171 ( 555) covalent geometry : angle 0.33145 ( 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 15 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.059 Fit side-chains REVERT: A 53 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8176 (tpt) outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 1.2000 time to fit residues: 16.9646 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=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: 1.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.122288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.109605 restraints weight = 584.117| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.30 r_work: 0.3217 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 1.0700 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= 0.089 Angle : 0.335 4.684 741 Z= 0.171 Chirality : 0.033 0.089 81 Planarity : 0.003 0.022 87 Dihedral : 12.616 50.331 115 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.34 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: 4.20 (1.00), residues: 67 helix: 3.49 (0.64), residues: 57 sheet: None (None), residues: 0 loop : -2.08 (1.64), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 11 PHE 0.005 0.001 PHE A 7 TYR 0.006 0.001 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00030 ( 1) link_TRANS : angle 0.34726 ( 3) hydrogen bonds : bond 0.02921 ( 42) hydrogen bonds : angle 3.81669 ( 126) covalent geometry : bond 0.00172 ( 555) covalent geometry : angle 0.33484 ( 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 : 0.062 Fit side-chains REVERT: A 53 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8175 (tpt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 1.2323 time to fit residues: 16.1922 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=2.50 ------------------------------------------------------------------------------- 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: 1.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7650 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.123251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111059 restraints weight = 565.355| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.23 r_work: 0.3225 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 1.0637 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= 0.085 Angle : 0.333 4.720 741 Z= 0.172 Chirality : 0.034 0.090 81 Planarity : 0.003 0.022 87 Dihedral : 12.493 51.840 115 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 5.34 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: 4.40 (1.01), residues: 67 helix: 3.64 (0.65), residues: 57 sheet: None (None), residues: 0 loop : -2.11 (1.59), 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 0.005 0.001 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00054 ( 1) link_TRANS : angle 0.20001 ( 3) hydrogen bonds : bond 0.02733 ( 42) hydrogen bonds : angle 3.79014 ( 126) covalent geometry : bond 0.00164 ( 555) covalent geometry : angle 0.33293 ( 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 15 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.062 Fit side-chains REVERT: A 53 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8064 (tpt) outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 1.1836 time to fit residues: 16.7449 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 ------------------------------------------------------------------------------- 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: 0.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.3323 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.119870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107585 restraints weight = 609.773| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.29 r_work: 0.3172 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 1.0678 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= 0.109 Angle : 0.358 4.718 741 Z= 0.182 Chirality : 0.034 0.088 81 Planarity : 0.003 0.022 87 Dihedral : 13.079 51.963 115 Min Nonbonded Distance : 2.632 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: 4.21 (1.02), residues: 67 helix: 3.50 (0.66), residues: 57 sheet: None (None), residues: 0 loop : -2.11 (1.59), 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 0.007 0.002 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00124 ( 1) link_TRANS : angle 0.16985 ( 3) hydrogen bonds : bond 0.03273 ( 42) hydrogen bonds : angle 3.98390 ( 126) covalent geometry : bond 0.00222 ( 555) covalent geometry : angle 0.35859 ( 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 : 0.064 Fit side-chains REVERT: A 53 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8028 (tpt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 1.2723 time to fit residues: 16.7105 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 : 0.063 ------------------------------------------------------------------------------- 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: 1.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.2987 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.120193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108559 restraints weight = 582.872| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.24 r_work: 0.3188 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 1.0707 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= 0.109 Angle : 0.363 4.761 741 Z= 0.188 Chirality : 0.035 0.091 81 Planarity : 0.003 0.021 87 Dihedral : 13.161 56.632 115 Min Nonbonded Distance : 2.632 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: 4.27 (1.02), residues: 67 helix: 3.55 (0.66), residues: 57 sheet: None (None), residues: 0 loop : -2.16 (1.57), 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 0.007 0.002 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00120 ( 1) link_TRANS : angle 0.17572 ( 3) hydrogen bonds : bond 0.03135 ( 42) hydrogen bonds : angle 3.94207 ( 126) covalent geometry : bond 0.00222 ( 555) covalent geometry : angle 0.36345 ( 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 : 0.067 Fit side-chains REVERT: A 53 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8036 (tpt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 1.2911 time to fit residues: 16.9590 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=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: 2.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.6657 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.116922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.104892 restraints weight = 585.451| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.27 r_work: 0.3141 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 1.0724 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= 0.178 Angle : 0.429 4.777 741 Z= 0.216 Chirality : 0.037 0.093 81 Planarity : 0.003 0.022 87 Dihedral : 14.328 56.653 115 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.34 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: 3.80 (1.01), residues: 67 helix: 3.20 (0.65), residues: 57 sheet: None (None), residues: 0 loop : -2.09 (1.63), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 11 PHE 0.008 0.002 PHE A 37 TYR 0.012 0.003 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00320 ( 1) link_TRANS : angle 0.15165 ( 3) hydrogen bonds : bond 0.04006 ( 42) hydrogen bonds : angle 4.16573 ( 126) covalent geometry : bond 0.00389 ( 555) covalent geometry : angle 0.42960 ( 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 : 0.065 Fit side-chains REVERT: A 53 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8000 (tpt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 1.2804 time to fit residues: 16.8176 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 : 0.057 ------------------------------------------------------------------------------- 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: 0.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 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 = 0.3441 r_free = 0.3441 target = 0.118273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106273 restraints weight = 586.159| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.27 r_work: 0.3162 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 1.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 556 Z= 0.144 Angle : 0.396 4.731 741 Z= 0.201 Chirality : 0.036 0.091 81 Planarity : 0.003 0.023 87 Dihedral : 13.860 50.293 115 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.34 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: 3.79 (1.01), residues: 67 helix: 3.18 (0.65), residues: 57 sheet: None (None), residues: 0 loop : -2.00 (1.63), 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 37 TYR 0.009 0.002 TYR A 13 Details of bonding type rmsd link_TRANS : bond 0.00212 ( 1) link_TRANS : angle 0.12209 ( 3) hydrogen bonds : bond 0.03701 ( 42) hydrogen bonds : angle 4.08231 ( 126) covalent geometry : bond 0.00308 ( 555) covalent geometry : angle 0.39708 ( 738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 843.94 seconds wall clock time: 15 minutes 25.98 seconds (925.98 seconds total)