Starting phenix.real_space_refine on Wed Mar 5 14:17:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ku5_23034/03_2025/7ku5_23034.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ku5_23034/03_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_23034/03_2025/7ku5_23034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ku5_23034/03_2025/7ku5_23034.map" model { file = "/net/cci-nas-00/data/ceres_data/7ku5_23034/03_2025/7ku5_23034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ku5_23034/03_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-5624/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: 1.64, per 1000 atoms: 2.19 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: 0.28 Conformation dependent library (CDL) restraints added in 90.8 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: 0.09 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: 0.14 Time building geometry restraints manager: 0.32 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: 0.890 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.800 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.780 ------------------------------------------------------------------------------- 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 : 0.076 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1537 time to fit residues: 2.5219 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 : 0.077 ------------------------------------------------------------------------------- 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: 2.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.4990 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.174472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.164065 restraints weight = 1636.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.165979 restraints weight = 965.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.167591 restraints weight = 660.077| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 799 Z= 0.348 Angle : 0.830 6.413 1133 Z= 0.413 Chirality : 0.056 0.169 97 Planarity : 0.007 0.054 153 Dihedral : 7.361 23.694 99 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % 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: -4.33 (0.82), residues: 86 helix: -2.85 (0.58), residues: 45 sheet: None (None), residues: 0 loop : -2.85 (1.05), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 116 HIS 0.003 0.001 HIS O 121 PHE 0.016 0.002 PHE O 92 TYR 0.007 0.002 TYR O 142 ARG 0.004 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 18 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.069 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 0.1099 time to fit residues: 2.0939 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 : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 5 optimal weight: 0.0000 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.8238 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.182154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.172185 restraints weight = 1587.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174634 restraints weight = 859.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.176298 restraints weight = 566.048| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 799 Z= 0.159 Angle : 0.661 6.172 1133 Z= 0.318 Chirality : 0.050 0.186 97 Planarity : 0.006 0.046 153 Dihedral : 6.659 21.538 99 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 5.00 % Allowed : 13.33 % 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: -3.61 (0.85), residues: 86 helix: -2.01 (0.61), residues: 45 sheet: None (None), residues: 0 loop : -2.83 (1.09), residues: 41 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 0.016 0.001 PHE O 92 TYR 0.003 0.001 TYR O 142 ARG 0.002 0.000 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 17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.078 Fit side-chains REVERT: O 142 TYR cc_start: 0.7683 (m-80) cc_final: 0.7127 (m-80) outliers start: 3 outliers final: 2 residues processed: 15 average time/residue: 0.0606 time to fit residues: 1.1297 Evaluate side-chains 15 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 111 SER 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: 0.3980 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6730 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.182226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.172400 restraints weight = 1578.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.174929 restraints weight = 816.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.176690 restraints weight = 516.907| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.3886 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= 0.152 Angle : 0.625 6.076 1133 Z= 0.303 Chirality : 0.048 0.153 97 Planarity : 0.006 0.042 153 Dihedral : 6.303 19.320 99 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 5.00 % Allowed : 11.67 % 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: -2.74 (0.90), residues: 86 helix: -1.00 (0.70), residues: 46 sheet: None (None), residues: 0 loop : -2.85 (1.10), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 74 HIS 0.000 0.000 HIS O 102 PHE 0.013 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 18 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.076 Fit side-chains REVERT: O 142 TYR cc_start: 0.7609 (m-80) cc_final: 0.7063 (m-80) outliers start: 3 outliers final: 2 residues processed: 16 average time/residue: 0.0559 time to fit residues: 1.1172 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 : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 111 SER 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: 0.0040 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.179143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.170722 restraints weight = 1621.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.172760 restraints weight = 838.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.174111 restraints weight = 522.979| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 799 Z= 0.146 Angle : 0.588 6.059 1133 Z= 0.283 Chirality : 0.048 0.142 97 Planarity : 0.006 0.042 153 Dihedral : 6.057 19.145 99 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 5.00 % Allowed : 16.67 % Favored : 78.33 % 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: -2.42 (0.92), residues: 86 helix: -0.70 (0.72), residues: 46 sheet: None (None), residues: 0 loop : -2.75 (1.12), residues: 40 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 0.010 0.001 PHE O 92 TYR 0.003 0.001 TYR O 142 ARG 0.000 0.000 ARG O 62 *********************** 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 19 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.079 Fit side-chains REVERT: O 114 TRP cc_start: 0.6852 (m-90) cc_final: 0.6491 (m-10) REVERT: O 142 TYR cc_start: 0.7560 (m-80) cc_final: 0.7032 (m-80) outliers start: 3 outliers final: 2 residues processed: 17 average time/residue: 0.0619 time to fit residues: 1.2869 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 : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 111 SER 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: 0.4980 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 0.0470 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 overall best weight: 0.5353 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.180902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.172448 restraints weight = 1604.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.174581 restraints weight = 801.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.175870 restraints weight = 482.649| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 799 Z= 0.141 Angle : 0.580 6.062 1133 Z= 0.281 Chirality : 0.046 0.134 97 Planarity : 0.005 0.041 153 Dihedral : 5.879 18.942 99 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 5.00 % Allowed : 16.67 % Favored : 78.33 % 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: -2.30 (0.94), residues: 86 helix: -1.04 (0.68), residues: 52 sheet: None (None), residues: 0 loop : -2.19 (1.31), residues: 34 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 0.009 0.001 PHE O 92 TYR 0.002 0.001 TYR O 142 ARG 0.001 0.000 ARG O 138 *********************** 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 18 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.078 Fit side-chains REVERT: O 114 TRP cc_start: 0.6745 (m-90) cc_final: 0.4453 (p-90) REVERT: O 142 TYR cc_start: 0.7527 (m-80) cc_final: 0.7169 (m-80) outliers start: 3 outliers final: 3 residues processed: 17 average time/residue: 0.0596 time to fit residues: 1.2521 Evaluate side-chains 17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 111 SER 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: 0.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.6735 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.170220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.159970 restraints weight = 1546.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.162715 restraints weight = 785.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.164323 restraints weight = 477.068| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 799 Z= 0.225 Angle : 0.646 6.237 1133 Z= 0.326 Chirality : 0.052 0.128 97 Planarity : 0.006 0.039 153 Dihedral : 6.288 18.430 99 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 5.00 % Allowed : 15.00 % 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: -2.46 (0.91), residues: 86 helix: -0.74 (0.70), residues: 46 sheet: None (None), residues: 0 loop : -2.77 (1.12), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 74 HIS 0.001 0.000 HIS O 121 PHE 0.010 0.002 PHE O 135 TYR 0.007 0.002 TYR O 142 ARG 0.001 0.000 ARG O 138 *********************** 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 18 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.079 Fit side-chains REVERT: O 114 TRP cc_start: 0.7269 (m-90) cc_final: 0.4672 (p-90) REVERT: O 142 TYR cc_start: 0.7787 (m-80) cc_final: 0.7350 (m-80) outliers start: 3 outliers final: 2 residues processed: 16 average time/residue: 0.0640 time to fit residues: 1.2568 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 : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 111 SER 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: 9.9990 chunk 2 optimal weight: 0.0170 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.0030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.177804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.169344 restraints weight = 1556.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.171648 restraints weight = 768.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.173104 restraints weight = 454.299| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4819 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= 0.172 Angle : 0.597 5.856 1133 Z= 0.298 Chirality : 0.047 0.116 97 Planarity : 0.005 0.039 153 Dihedral : 6.092 18.685 99 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 10.16 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: -2.28 (0.93), residues: 86 helix: -0.48 (0.72), residues: 46 sheet: None (None), residues: 0 loop : -2.84 (1.11), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 74 HIS 0.001 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 138 *********************** 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 19 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.077 Fit side-chains REVERT: O 114 TRP cc_start: 0.7188 (m-90) cc_final: 0.4796 (p-90) REVERT: O 142 TYR cc_start: 0.7666 (m-80) cc_final: 0.7209 (m-80) outliers start: 2 outliers final: 2 residues processed: 18 average time/residue: 0.0627 time to fit residues: 1.3630 Evaluate side-chains 18 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 111 SER 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: 0.0270 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6303 ------------------------------------------------------------------------------- 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 = 0.177597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.169013 restraints weight = 1568.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.171351 restraints weight = 757.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.172784 restraints weight = 447.013| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 799 Z= 0.153 Angle : 0.592 5.880 1133 Z= 0.289 Chirality : 0.045 0.116 97 Planarity : 0.005 0.039 153 Dihedral : 5.846 17.810 99 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % 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: -2.26 (0.95), residues: 86 helix: -0.90 (0.69), residues: 52 sheet: None (None), residues: 0 loop : -2.36 (1.29), residues: 34 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 0.001 0.000 TYR O 142 ARG 0.001 0.000 ARG O 62 *********************** 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 17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.075 Fit side-chains REVERT: O 114 TRP cc_start: 0.7019 (m-90) cc_final: 0.4578 (p-90) REVERT: O 142 TYR cc_start: 0.7606 (m-80) cc_final: 0.7200 (m-80) outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.0569 time to fit residues: 1.1433 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 : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 111 SER 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: 0.0020 chunk 2 optimal weight: 0.2980 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 overall best weight: 0.3490 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.185383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.177627 restraints weight = 1432.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.179591 restraints weight = 771.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.180669 restraints weight = 480.198| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 799 Z= 0.143 Angle : 0.557 5.646 1133 Z= 0.277 Chirality : 0.043 0.116 97 Planarity : 0.005 0.038 153 Dihedral : 5.614 18.510 99 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 3.33 % Allowed : 18.33 % Favored : 78.33 % 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: -1.77 (1.01), residues: 86 helix: -0.71 (0.72), residues: 51 sheet: None (None), residues: 0 loop : -1.77 (1.38), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 74 HIS 0.000 0.000 HIS O 121 PHE 0.008 0.001 PHE O 92 TYR 0.001 0.000 TYR O 142 ARG 0.001 0.000 ARG O 61 ********************** 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 18 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.075 Fit side-chains REVERT: O 114 TRP cc_start: 0.6759 (m-90) cc_final: 0.4630 (p-90) REVERT: O 142 TYR cc_start: 0.7371 (m-80) cc_final: 0.7055 (m-80) outliers start: 2 outliers final: 2 residues processed: 18 average time/residue: 0.0587 time to fit residues: 1.2914 Evaluate side-chains 18 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 111 SER 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: 5.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 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 = 0.4099 r_free = 0.4099 target = 0.176665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.167068 restraints weight = 1446.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.169307 restraints weight = 706.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.170742 restraints weight = 433.673| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 799 Z= 0.156 Angle : 0.586 5.921 1133 Z= 0.287 Chirality : 0.045 0.118 97 Planarity : 0.005 0.039 153 Dihedral : 5.511 18.644 99 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.95 % Favored : 86.05 % Rotamer: Outliers : 3.33 % Allowed : 20.00 % 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: -1.70 (1.01), residues: 86 helix: -0.62 (0.73), residues: 51 sheet: None (None), residues: 0 loop : -1.79 (1.38), 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 0.007 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: 670.29 seconds wall clock time: 12 minutes 13.10 seconds (733.10 seconds total)