Starting phenix.real_space_refine on Mon Feb 10 19:27:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ku5_23034/02_2025/7ku5_23034.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ku5_23034/02_2025/7ku5_23034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ku5_23034/02_2025/7ku5_23034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ku5_23034/02_2025/7ku5_23034.map" model { file = "/net/cci-nas-00/data/ceres_data/7ku5_23034/02_2025/7ku5_23034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ku5_23034/02_2025/7ku5_23034.cif" } resolution = 3.76 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= -0.000 sd= 0.153 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 Mg 3 5.21 5 S 1 5.16 5 C 512 2.51 5 N 125 2.21 5 O 109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 750 Number of models: 1 Model: "" Number of chains: 2 Chain: "O" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 655 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 81} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "O" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 95 Unusual residues: {'BCR': 1, 'CLA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'BCR:plan-2': 1, 'CLA:plan-2': 3, 'CLA:plan-3': 3, 'CLA:plan-4': 3, 'CLA:plan-5': 3, 'CLA:plan-6': 3, 'BCR:plan-5': 1, 'BCR:plan-4': 1, 'BCR:plan-7': 1, 'BCR:plan-6': 1, 'BCR:plan-3': 1, 'BCR:plan-8': 1} Unresolved non-hydrogen planarities: 91 Time building chain proxies: 1.96, per 1000 atoms: 2.61 Number of scatterers: 750 At special positions: 0 Unit cell: (52, 35.36, 62.4, 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 1 16.00 Mg 3 11.99 O 109 8.00 N 125 7.00 C 512 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 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 113.9 milliseconds 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 150 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 0 sheets defined 56.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'O' and resid 65 through 73 Processing helix chain 'O' and resid 83 through 87 removed outlier: 4.109A pdb=" N SER O 87 " --> pdb=" O ASN O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 101 removed outlier: 3.623A pdb=" N GLU O 99 " --> pdb=" O SER O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 128 removed outlier: 4.374A pdb=" N TRP O 116 " --> pdb=" O PRO O 112 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL O 118 " --> pdb=" O TRP O 114 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL O 122 " --> pdb=" O VAL O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 140 removed outlier: 3.503A pdb=" N ILE O 133 " --> pdb=" O THR O 129 " (cutoff:3.500A) 25 hydrogen bonds defined for protein. 72 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: 0.16 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 335 1.40 - 1.57: 450 1.57 - 1.75: 0 1.75 - 1.92: 2 1.92 - 2.09: 12 Bond restraints: 799 Sorted by residual: bond pdb=" C GLY O 106 " pdb=" N PRO O 107 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.93e+00 bond pdb=" N THR O 105 " pdb=" CA THR O 105 " ideal model delta sigma weight residual 1.462 1.489 -0.027 1.48e-02 4.57e+03 3.42e+00 bond pdb=" N TRP O 114 " pdb=" CA TRP O 114 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.33e+00 bond pdb=" C25 BCR O 301 " pdb=" C30 BCR O 301 " ideal model delta sigma weight residual 1.532 1.496 0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" CB TRP O 114 " pdb=" CG TRP O 114 " ideal model delta sigma weight residual 1.498 1.452 0.046 3.10e-02 1.04e+03 2.25e+00 ... (remaining 794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 1069 2.51 - 5.03: 50 5.03 - 7.54: 9 7.54 - 10.06: 4 10.06 - 12.57: 1 Bond angle restraints: 1133 Sorted by residual: angle pdb=" C PRO O 104 " pdb=" N THR O 105 " pdb=" CA THR O 105 " ideal model delta sigma weight residual 122.61 129.47 -6.86 1.56e+00 4.11e-01 1.93e+01 angle pdb=" C TRP O 114 " pdb=" CA TRP O 114 " pdb=" CB TRP O 114 " ideal model delta sigma weight residual 110.42 102.99 7.43 1.99e+00 2.53e-01 1.39e+01 angle pdb=" CA LEU O 91 " pdb=" CB LEU O 91 " pdb=" CG LEU O 91 " ideal model delta sigma weight residual 116.30 128.87 -12.57 3.50e+00 8.16e-02 1.29e+01 angle pdb=" N TRP O 114 " pdb=" CA TRP O 114 " pdb=" CB TRP O 114 " ideal model delta sigma weight residual 110.49 116.45 -5.96 1.69e+00 3.50e-01 1.24e+01 angle pdb=" N TRP O 114 " pdb=" CA TRP O 114 " pdb=" C TRP O 114 " ideal model delta sigma weight residual 110.80 118.02 -7.22 2.13e+00 2.20e-01 1.15e+01 ... (remaining 1128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 332 17.20 - 34.39: 36 34.39 - 51.59: 5 51.59 - 68.79: 0 68.79 - 85.98: 1 Dihedral angle restraints: 374 sinusoidal: 136 harmonic: 238 Sorted by residual: dihedral pdb=" CA GLY O 106 " pdb=" C GLY O 106 " pdb=" N PRO O 107 " pdb=" CA PRO O 107 " ideal model delta harmonic sigma weight residual -180.00 -155.26 -24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA TRP O 74 " pdb=" C TRP O 74 " pdb=" N LEU O 75 " pdb=" CA LEU O 75 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PHE O 92 " pdb=" C PHE O 92 " pdb=" N LEU O 93 " pdb=" CA LEU O 93 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 49 0.046 - 0.091: 33 0.091 - 0.137: 10 0.137 - 0.182: 2 0.182 - 0.228: 3 Chirality restraints: 97 Sorted by residual: chirality pdb=" CA TRP O 114 " pdb=" N TRP O 114 " pdb=" C TRP O 114 " pdb=" CB TRP O 114 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA LEU O 91 " pdb=" N LEU O 91 " pdb=" C LEU O 91 " pdb=" CB LEU O 91 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" CA THR O 105 " pdb=" N THR O 105 " pdb=" C THR O 105 " pdb=" CB THR O 105 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 94 not shown) Planarity restraints: 153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND CLA O 201 " 0.064 2.00e-02 2.50e+03 4.55e-02 3.10e+01 pdb=" C1A CLA O 201 " -0.028 2.00e-02 2.50e+03 pdb=" C3D CLA O 201 " -0.045 2.00e-02 2.50e+03 pdb=" C4D CLA O 201 " -0.039 2.00e-02 2.50e+03 pdb=" CBD CLA O 201 " 0.061 2.00e-02 2.50e+03 pdb=" CHA CLA O 201 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 114 " 0.037 2.00e-02 2.50e+03 2.78e-02 1.93e+01 pdb=" CG TRP O 114 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP O 114 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP O 114 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP O 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP O 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP O 114 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 114 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 114 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP O 114 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA O 203 " -0.019 2.00e-02 2.50e+03 3.56e-02 1.90e+01 pdb=" C2A CLA O 203 " 0.058 2.00e-02 2.50e+03 pdb=" C4A CLA O 203 " -0.032 2.00e-02 2.50e+03 pdb=" CHA CLA O 203 " -0.023 2.00e-02 2.50e+03 pdb=" NA CLA O 203 " -0.026 2.00e-02 2.50e+03 pdb="MG CLA O 203 " 0.041 2.00e-02 2.50e+03 ... (remaining 150 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 252 2.92 - 3.41: 653 3.41 - 3.91: 1118 3.91 - 4.40: 1191 4.40 - 4.90: 1854 Nonbonded interactions: 5068 Sorted by model distance: nonbonded pdb=" NH1 ARG O 61 " pdb=" OE1 GLN O 132 " model vdw 2.420 3.120 nonbonded pdb=" NZ LYS O 136 " pdb=" OD2 ASP O 140 " model vdw 2.502 3.120 nonbonded pdb=" O LEU O 75 " pdb=" OG SER O 79 " model vdw 2.510 3.040 nonbonded pdb=" O LEU O 91 " pdb=" N SER O 95 " model vdw 2.525 3.120 nonbonded pdb=" O ASP O 63 " pdb=" N SER O 65 " model vdw 2.582 3.120 ... (remaining 5063 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.270 Find NCS groups from input model: 0.010 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:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 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 0.052 799 Z= 0.382 Angle : 1.290 12.573 1133 Z= 0.648 Chirality : 0.068 0.228 97 Planarity : 0.013 0.066 153 Dihedral : 14.852 85.984 224 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -5.41 (0.71), residues: 86 helix: -4.07 (0.40), residues: 40 sheet: None (None), residues: 0 loop : -3.17 (0.90), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP O 114 HIS 0.002 0.001 HIS O 121 PHE 0.022 0.002 PHE O 92 TYR 0.008 0.002 TYR O 142 ARG 0.024 0.008 ARG O 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.074 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1561 time to fit residues: 2.5575 Evaluate side-chains 12 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 1.9485 ------------------------------------------------------------------------------- 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 = 0.4151 r_free = 0.4151 target = 0.178733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.167840 restraints weight = 1610.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.170178 restraints weight = 930.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.171446 restraints weight = 634.646| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 799 Z= 0.286 Angle : 0.766 6.362 1133 Z= 0.380 Chirality : 0.053 0.157 97 Planarity : 0.007 0.054 153 Dihedral : 7.104 23.742 99 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 1.67 % Allowed : 10.00 % Favored : 88.33 % 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: -4.25 (0.83), residues: 86 helix: -2.70 (0.61), residues: 45 sheet: None (None), residues: 0 loop : -2.93 (1.04), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 116 HIS 0.002 0.001 HIS O 121 PHE 0.016 0.002 PHE O 92 TYR 0.006 0.002 TYR O 142 ARG 0.003 0.001 ARG O 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.058 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.1204 time to fit residues: 2.1399 Evaluate side-chains 15 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 75 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 1.0983 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.177793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.167164 restraints weight = 1584.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.169464 restraints weight = 834.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.171087 restraints weight = 538.596| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 799 Z= 0.180 Angle : 0.656 6.266 1133 Z= 0.320 Chirality : 0.048 0.146 97 Planarity : 0.006 0.045 153 Dihedral : 6.645 21.787 99 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % Rotamer: Outliers : 3.33 % Allowed : 8.33 % Favored : 88.33 % 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: -3.56 (0.86), residues: 86 helix: -1.89 (0.63), residues: 45 sheet: None (None), residues: 0 loop : -2.92 (1.09), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 74 HIS 0.000 0.000 HIS O 121 PHE 0.015 0.001 PHE O 92 TYR 0.005 0.001 TYR O 142 ARG 0.003 0.001 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.072 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 12 average time/residue: 0.0562 time to fit residues: 0.8734 Evaluate side-chains 13 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 75 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.0270 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.5553 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.176751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.167297 restraints weight = 1609.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.169742 restraints weight = 826.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.171215 restraints weight = 516.124| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 799 Z= 0.142 Angle : 0.595 6.011 1133 Z= 0.286 Chirality : 0.047 0.118 97 Planarity : 0.006 0.043 153 Dihedral : 6.171 18.354 99 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.33 % Allowed : 8.33 % Favored : 88.33 % 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: -2.85 (0.90), residues: 86 helix: -1.05 (0.70), residues: 45 sheet: None (None), residues: 0 loop : -2.94 (1.08), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 74 HIS 0.000 0.000 HIS O 102 PHE 0.012 0.001 PHE O 92 TYR 0.002 0.001 TYR O 142 ARG 0.002 0.000 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.077 Fit side-chains REVERT: O 142 TYR cc_start: 0.7661 (m-80) cc_final: 0.7176 (m-80) outliers start: 2 outliers final: 0 residues processed: 14 average time/residue: 0.0581 time to fit residues: 1.0250 Evaluate side-chains 14 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.175776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.166615 restraints weight = 1601.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.168988 restraints weight = 809.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.170354 restraints weight = 496.307| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 799 Z= 0.148 Angle : 0.602 6.028 1133 Z= 0.286 Chirality : 0.049 0.168 97 Planarity : 0.006 0.042 153 Dihedral : 6.108 19.665 99 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 1.67 % Allowed : 16.67 % Favored : 81.67 % 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: -2.39 (0.93), residues: 86 helix: -0.61 (0.72), residues: 46 sheet: None (None), residues: 0 loop : -2.83 (1.11), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 74 HIS 0.001 0.000 HIS O 121 PHE 0.010 0.001 PHE O 92 TYR 0.004 0.001 TYR O 142 ARG 0.001 0.000 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.072 Fit side-chains REVERT: O 114 TRP cc_start: 0.6976 (m-90) cc_final: 0.6533 (m-10) REVERT: O 142 TYR cc_start: 0.7684 (m-80) cc_final: 0.7219 (m-80) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.0585 time to fit residues: 1.1602 Evaluate side-chains 15 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.0270 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6805 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.179316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.171174 restraints weight = 1623.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.173262 restraints weight = 801.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.174640 restraints weight = 485.498| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 799 Z= 0.148 Angle : 0.578 5.893 1133 Z= 0.279 Chirality : 0.047 0.136 97 Planarity : 0.005 0.041 153 Dihedral : 5.963 19.194 99 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.33 % Allowed : 15.00 % Favored : 81.67 % 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: -2.23 (0.92), residues: 86 helix: -0.49 (0.70), residues: 46 sheet: None (None), residues: 0 loop : -2.75 (1.12), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 74 HIS 0.000 0.000 HIS O 121 PHE 0.008 0.001 PHE O 92 TYR 0.003 0.001 TYR O 142 ARG 0.001 0.000 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.068 Fit side-chains REVERT: O 114 TRP cc_start: 0.6937 (m-90) cc_final: 0.6515 (m-10) REVERT: O 142 TYR cc_start: 0.7624 (m-80) cc_final: 0.7296 (m-80) outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.0578 time to fit residues: 1.1433 Evaluate side-chains 16 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 82 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.167804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.158005 restraints weight = 1502.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.160377 restraints weight = 739.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.161654 restraints weight = 455.300| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 799 Z= 0.270 Angle : 0.673 6.133 1133 Z= 0.342 Chirality : 0.054 0.133 97 Planarity : 0.006 0.039 153 Dihedral : 6.612 18.168 99 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 3.33 % Allowed : 13.33 % Favored : 83.33 % 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: -2.72 (0.89), residues: 86 helix: -0.95 (0.69), residues: 46 sheet: None (None), residues: 0 loop : -2.90 (1.07), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP O 116 HIS 0.001 0.000 HIS O 102 PHE 0.015 0.002 PHE O 135 TYR 0.009 0.003 TYR O 142 ARG 0.003 0.001 ARG O 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.075 Fit side-chains REVERT: O 114 TRP cc_start: 0.7396 (m-90) cc_final: 0.4617 (p-90) REVERT: O 142 TYR cc_start: 0.7872 (m-80) cc_final: 0.7388 (m-80) outliers start: 2 outliers final: 1 residues processed: 14 average time/residue: 0.0684 time to fit residues: 1.1714 Evaluate side-chains 14 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 overall best weight: 2.1235 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.171699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.162293 restraints weight = 1525.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.164539 restraints weight = 744.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.166056 restraints weight = 454.870| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 799 Z= 0.259 Angle : 0.700 5.755 1133 Z= 0.353 Chirality : 0.051 0.130 97 Planarity : 0.006 0.040 153 Dihedral : 6.410 16.648 99 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 3.33 % Allowed : 16.67 % Favored : 80.00 % 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: -3.00 (0.87), residues: 86 helix: -1.07 (0.67), residues: 45 sheet: None (None), residues: 0 loop : -3.14 (1.05), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 74 HIS 0.001 0.001 HIS O 121 PHE 0.009 0.002 PHE O 135 TYR 0.005 0.002 TYR O 142 ARG 0.002 0.000 ARG O 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.068 Fit side-chains REVERT: O 114 TRP cc_start: 0.7201 (m-90) cc_final: 0.4712 (p-90) REVERT: O 142 TYR cc_start: 0.7852 (m-80) cc_final: 0.7335 (m-80) outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.0646 time to fit residues: 1.1773 Evaluate side-chains 17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6230 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.177847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.169362 restraints weight = 1521.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.171550 restraints weight = 743.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.172806 restraints weight = 438.105| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 799 Z= 0.151 Angle : 0.587 5.603 1133 Z= 0.292 Chirality : 0.046 0.115 97 Planarity : 0.006 0.040 153 Dihedral : 6.135 16.999 99 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 1.67 % Allowed : 18.33 % Favored : 80.00 % 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: -2.27 (0.95), residues: 86 helix: -0.42 (0.74), residues: 46 sheet: None (None), residues: 0 loop : -2.91 (1.12), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 74 HIS 0.001 0.000 HIS O 121 PHE 0.009 0.001 PHE O 92 TYR 0.001 0.000 TYR O 142 ARG 0.001 0.000 ARG O 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.070 Fit side-chains REVERT: O 114 TRP cc_start: 0.6984 (m-90) cc_final: 0.4630 (p-90) REVERT: O 142 TYR cc_start: 0.7707 (m-80) cc_final: 0.7262 (m-80) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.0612 time to fit residues: 1.2610 Evaluate side-chains 17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.0170 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.181819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.174019 restraints weight = 1437.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.175896 restraints weight = 776.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.177121 restraints weight = 493.789| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 799 Z= 0.143 Angle : 0.582 5.695 1133 Z= 0.280 Chirality : 0.044 0.117 97 Planarity : 0.005 0.040 153 Dihedral : 5.617 17.956 99 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 1.67 % Allowed : 18.33 % Favored : 80.00 % 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: -2.00 (0.99), residues: 86 helix: -0.88 (0.71), residues: 51 sheet: None (None), residues: 0 loop : -1.89 (1.36), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 74 HIS 0.000 0.000 HIS O 121 PHE 0.008 0.001 PHE O 92 TYR 0.002 0.000 TYR O 142 ARG 0.001 0.000 ARG O 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.076 Fit side-chains REVERT: O 114 TRP cc_start: 0.6710 (m-90) cc_final: 0.4693 (p-90) REVERT: O 142 TYR cc_start: 0.7480 (m-80) cc_final: 0.7128 (m-80) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.0603 time to fit residues: 1.2529 Evaluate side-chains 17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.177203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.167617 restraints weight = 1451.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.169848 restraints weight = 735.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.171301 restraints weight = 459.450| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 799 Z= 0.159 Angle : 0.594 5.711 1133 Z= 0.299 Chirality : 0.045 0.117 97 Planarity : 0.006 0.040 153 Dihedral : 5.610 18.193 99 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 1.67 % Allowed : 21.67 % Favored : 76.67 % 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: -1.88 (1.00), residues: 86 helix: -0.77 (0.73), residues: 51 sheet: None (None), residues: 0 loop : -1.87 (1.35), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 74 HIS 0.001 0.000 HIS O 121 PHE 0.010 0.001 PHE O 92 TYR 0.002 0.001 TYR O 142 ARG 0.001 0.000 ARG O 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 670.20 seconds wall clock time: 12 minutes 33.07 seconds (753.07 seconds total)