Starting phenix.real_space_refine on Wed Jun 4 11:34:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fa1_28947/06_2025/8fa1_28947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fa1_28947/06_2025/8fa1_28947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fa1_28947/06_2025/8fa1_28947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fa1_28947/06_2025/8fa1_28947.map" model { file = "/net/cci-nas-00/data/ceres_data/8fa1_28947/06_2025/8fa1_28947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fa1_28947/06_2025/8fa1_28947.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 3 Type Number sf(0) Gaussians C 1572 2.51 5 N 447 2.21 5 O 534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 2553 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 532 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "E" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Restraints were copied for chains: C, B, D, F Time building chain proxies: 1.89, per 1000 atoms: 0.74 Number of scatterers: 2553 At special positions: 0 Unit cell: (47.436, 55.476, 118.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 534 8.00 N 447 7.00 C 1572 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: 0.58 Conformation dependent library (CDL) restraints added in 300.7 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 removed outlier: 3.776A pdb=" N LEU D1197 " --> pdb=" O ASN D1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1194 through 1197' Processing helix chain 'E' and resid 1179 through 1193 Processing helix chain 'E' and resid 1194 through 1197 removed outlier: 3.776A pdb=" N LEU E1197 " --> pdb=" O ASN E1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1194 through 1197' Processing helix chain 'F' and resid 1179 through 1193 Processing helix chain 'F' and resid 1194 through 1197 removed outlier: 3.776A pdb=" N LEU F1197 " --> pdb=" O ASN F1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1194 through 1197' 232 hydrogen bonds defined for protein. 696 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: 0.61 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 483 1.29 - 1.35: 417 1.35 - 1.42: 66 1.42 - 1.48: 378 1.48 - 1.54: 1215 Bond restraints: 2559 Sorted by residual: bond pdb=" CA ASN D1178 " pdb=" CB ASN D1178 " ideal model delta sigma weight residual 1.531 1.505 0.025 3.12e-02 1.03e+03 6.58e-01 bond pdb=" CA ASN F1178 " pdb=" CB ASN F1178 " ideal model delta sigma weight residual 1.531 1.505 0.025 3.12e-02 1.03e+03 6.49e-01 bond pdb=" CB VAL E1177 " pdb=" CG2 VAL E1177 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.48e-01 bond pdb=" CB VAL F1177 " pdb=" CG2 VAL F1177 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.42e-01 bond pdb=" CB VAL D1177 " pdb=" CG2 VAL D1177 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.30e-01 ... (remaining 2554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 3351 1.35 - 2.70: 79 2.70 - 4.04: 14 4.04 - 5.39: 3 5.39 - 6.74: 6 Bond angle restraints: 3453 Sorted by residual: angle pdb=" N ASN A 978 " pdb=" CA ASN A 978 " pdb=" CB ASN A 978 " ideal model delta sigma weight residual 110.16 113.84 -3.68 1.48e+00 4.57e-01 6.19e+00 angle pdb=" N ASN B 978 " pdb=" CA ASN B 978 " pdb=" CB ASN B 978 " ideal model delta sigma weight residual 110.16 113.84 -3.68 1.48e+00 4.57e-01 6.18e+00 angle pdb=" N ASN C 978 " pdb=" CA ASN C 978 " pdb=" CB ASN C 978 " ideal model delta sigma weight residual 110.16 113.83 -3.67 1.48e+00 4.57e-01 6.14e+00 angle pdb=" CA LEU B 962 " pdb=" CB LEU B 962 " pdb=" CG LEU B 962 " ideal model delta sigma weight residual 116.30 123.04 -6.74 3.50e+00 8.16e-02 3.71e+00 angle pdb=" CA LEU A 962 " pdb=" CB LEU A 962 " pdb=" CG LEU A 962 " ideal model delta sigma weight residual 116.30 122.99 -6.69 3.50e+00 8.16e-02 3.65e+00 ... (remaining 3448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 1368 14.97 - 29.94: 189 29.94 - 44.91: 21 44.91 - 59.88: 18 59.88 - 74.85: 9 Dihedral angle restraints: 1605 sinusoidal: 624 harmonic: 981 Sorted by residual: dihedral pdb=" N GLN C 957 " pdb=" CA GLN C 957 " pdb=" CB GLN C 957 " pdb=" CG GLN C 957 " ideal model delta sinusoidal sigma weight residual 180.00 -120.29 -59.71 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN B 957 " pdb=" CA GLN B 957 " pdb=" CB GLN B 957 " pdb=" CG GLN B 957 " ideal model delta sinusoidal sigma weight residual -180.00 -120.29 -59.71 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN A 957 " pdb=" CA GLN A 957 " pdb=" CB GLN A 957 " pdb=" CG GLN A 957 " ideal model delta sinusoidal sigma weight residual -180.00 -120.33 -59.67 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 255 0.027 - 0.053: 119 0.053 - 0.080: 36 0.080 - 0.106: 19 0.106 - 0.133: 6 Chirality restraints: 435 Sorted by residual: chirality pdb=" CA GLN A 920 " pdb=" N GLN A 920 " pdb=" C GLN A 920 " pdb=" CB GLN A 920 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA GLN B 920 " pdb=" N GLN B 920 " pdb=" C GLN B 920 " pdb=" CB GLN B 920 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA GLN C 920 " pdb=" N GLN C 920 " pdb=" C GLN C 920 " pdb=" CB GLN C 920 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 432 not shown) Planarity restraints: 453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 919 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C ASN A 919 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN A 919 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN A 920 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 919 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C ASN B 919 " -0.037 2.00e-02 2.50e+03 pdb=" O ASN B 919 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN B 920 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 919 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C ASN C 919 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN C 919 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN C 920 " -0.013 2.00e-02 2.50e+03 ... (remaining 450 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 703 2.81 - 3.33: 2762 3.33 - 3.85: 4259 3.85 - 4.38: 4728 4.38 - 4.90: 8073 Nonbonded interactions: 20525 Sorted by model distance: nonbonded pdb=" ND2 ASN C 978 " pdb=" OD1 ASP F1163 " model vdw 2.286 3.120 nonbonded pdb=" ND2 ASN B 978 " pdb=" OD1 ASP E1163 " model vdw 2.333 3.120 nonbonded pdb=" ND2 ASN A 978 " pdb=" OD1 ASP D1163 " model vdw 2.388 3.120 nonbonded pdb=" NE2 GLN C 935 " pdb=" O ALA F1190 " model vdw 2.418 3.120 nonbonded pdb=" NE2 GLN A 935 " pdb=" O ALA D1190 " model vdw 2.429 3.120 ... (remaining 20520 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.400 Find NCS groups from input model: 0.040 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 0.027 2559 Z= 0.259 Angle : 0.572 6.742 3453 Z= 0.296 Chirality : 0.039 0.133 435 Planarity : 0.004 0.034 453 Dihedral : 15.924 74.850 957 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % 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: 0.73 (0.42), residues: 327 helix: 1.08 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -1.33 (0.73), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.003 0.001 PHE A 927 ARG 0.004 0.001 ARG C 983 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 232) hydrogen bonds : angle 3.83599 ( 696) covalent geometry : bond 0.00553 ( 2559) covalent geometry : angle 0.57250 ( 3453) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.287 Fit side-chains REVERT: B 980 ILE cc_start: 0.8929 (mt) cc_final: 0.8713 (mt) REVERT: C 973 ILE cc_start: 0.9020 (mt) cc_final: 0.8778 (mt) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.4771 time to fit residues: 19.4062 Evaluate side-chains 37 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN E1159 HIS F1159 HIS F1173 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.147247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.129232 restraints weight = 3485.004| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.12 r_work: 0.3931 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2559 Z= 0.164 Angle : 0.466 7.260 3453 Z= 0.244 Chirality : 0.037 0.122 435 Planarity : 0.002 0.013 453 Dihedral : 3.347 11.744 339 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.03 % Allowed : 15.49 % Favored : 81.48 % 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: 3.49 (0.45), residues: 327 helix: 3.05 (0.29), residues: 252 sheet: None (None), residues: 0 loop : -0.41 (0.82), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.006 0.001 PHE C 970 ARG 0.003 0.001 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 232) hydrogen bonds : angle 3.14153 ( 696) covalent geometry : bond 0.00355 ( 2559) covalent geometry : angle 0.46551 ( 3453) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.336 Fit side-chains REVERT: C 973 ILE cc_start: 0.9117 (mt) cc_final: 0.8886 (mt) outliers start: 9 outliers final: 1 residues processed: 47 average time/residue: 0.4870 time to fit residues: 24.3421 Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1177 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 4 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.141325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.123055 restraints weight = 3528.499| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.20 r_work: 0.3916 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2559 Z= 0.164 Angle : 0.452 7.237 3453 Z= 0.234 Chirality : 0.037 0.132 435 Planarity : 0.002 0.012 453 Dihedral : 3.234 10.268 339 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.36 % Allowed : 17.17 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.33 (0.46), residues: 327 helix: 3.68 (0.29), residues: 252 sheet: None (None), residues: 0 loop : -0.24 (0.84), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.004 0.001 PHE A 927 ARG 0.003 0.001 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 232) hydrogen bonds : angle 2.93337 ( 696) covalent geometry : bond 0.00358 ( 2559) covalent geometry : angle 0.45187 ( 3453) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.303 Fit side-chains REVERT: C 973 ILE cc_start: 0.9064 (mt) cc_final: 0.8808 (mt) outliers start: 7 outliers final: 3 residues processed: 42 average time/residue: 0.4877 time to fit residues: 21.8701 Evaluate side-chains 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.141542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.123660 restraints weight = 3545.130| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.25 r_work: 0.3919 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2559 Z= 0.165 Angle : 0.448 7.271 3453 Z= 0.234 Chirality : 0.037 0.137 435 Planarity : 0.002 0.011 453 Dihedral : 3.197 10.196 339 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.03 % Allowed : 16.84 % Favored : 80.13 % 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: 4.58 (0.45), residues: 327 helix: 3.86 (0.28), residues: 252 sheet: None (None), residues: 0 loop : -0.18 (0.84), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.005 0.001 PHE A 927 ARG 0.002 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 232) hydrogen bonds : angle 2.87831 ( 696) covalent geometry : bond 0.00360 ( 2559) covalent geometry : angle 0.44798 ( 3453) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.282 Fit side-chains REVERT: A 962 LEU cc_start: 0.8808 (tm) cc_final: 0.8589 (tt) REVERT: C 973 ILE cc_start: 0.9077 (mt) cc_final: 0.8815 (mt) outliers start: 9 outliers final: 3 residues processed: 46 average time/residue: 0.6414 time to fit residues: 30.9479 Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.147338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.129429 restraints weight = 3469.290| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.13 r_work: 0.3951 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2559 Z= 0.165 Angle : 0.454 6.869 3453 Z= 0.238 Chirality : 0.038 0.147 435 Planarity : 0.002 0.012 453 Dihedral : 3.192 9.788 339 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.69 % Allowed : 16.16 % Favored : 81.14 % 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: 4.57 (0.45), residues: 327 helix: 3.90 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.16 (0.81), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.005 0.001 PHE A 927 ARG 0.003 0.001 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 232) hydrogen bonds : angle 2.90187 ( 696) covalent geometry : bond 0.00362 ( 2559) covalent geometry : angle 0.45438 ( 3453) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.288 Fit side-chains REVERT: C 962 LEU cc_start: 0.8781 (tm) cc_final: 0.8549 (tt) REVERT: C 973 ILE cc_start: 0.9111 (mt) cc_final: 0.8876 (mt) outliers start: 8 outliers final: 2 residues processed: 44 average time/residue: 0.5436 time to fit residues: 25.3147 Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain E residue 1177 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 0.0030 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.143402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.125250 restraints weight = 3574.767| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.21 r_work: 0.3948 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 2559 Z= 0.103 Angle : 0.426 6.734 3453 Z= 0.225 Chirality : 0.037 0.150 435 Planarity : 0.002 0.011 453 Dihedral : 2.966 9.033 339 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.36 % Allowed : 17.17 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.08 (0.45), residues: 327 helix: 4.27 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.01 (0.81), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.004 0.001 PHE A 927 ARG 0.002 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 232) hydrogen bonds : angle 2.77479 ( 696) covalent geometry : bond 0.00220 ( 2559) covalent geometry : angle 0.42561 ( 3453) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.266 Fit side-chains REVERT: C 973 ILE cc_start: 0.9074 (mt) cc_final: 0.8821 (mt) outliers start: 7 outliers final: 2 residues processed: 45 average time/residue: 0.5309 time to fit residues: 25.2586 Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4379 r_free = 0.4379 target = 0.141964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.123526 restraints weight = 3599.254| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 2.26 r_work: 0.3937 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 2559 Z= 0.151 Angle : 0.449 7.105 3453 Z= 0.239 Chirality : 0.038 0.163 435 Planarity : 0.002 0.011 453 Dihedral : 3.092 9.812 339 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.36 % Allowed : 17.17 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.85 (0.45), residues: 327 helix: 4.11 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.10 (0.81), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.004 0.001 PHE A 927 ARG 0.003 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 232) hydrogen bonds : angle 2.86411 ( 696) covalent geometry : bond 0.00337 ( 2559) covalent geometry : angle 0.44930 ( 3453) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.265 Fit side-chains REVERT: C 962 LEU cc_start: 0.8664 (tm) cc_final: 0.8422 (tt) REVERT: C 973 ILE cc_start: 0.9074 (mt) cc_final: 0.8814 (mt) outliers start: 7 outliers final: 4 residues processed: 43 average time/residue: 0.5491 time to fit residues: 24.9343 Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.141898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.123640 restraints weight = 3552.269| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.26 r_work: 0.3911 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2559 Z= 0.169 Angle : 0.461 6.772 3453 Z= 0.247 Chirality : 0.039 0.157 435 Planarity : 0.002 0.013 453 Dihedral : 3.186 10.257 339 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.36 % Allowed : 17.51 % Favored : 80.13 % 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: 4.69 (0.45), residues: 327 helix: 3.97 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.08 (0.80), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.005 0.001 PHE A 927 ARG 0.003 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 232) hydrogen bonds : angle 2.91977 ( 696) covalent geometry : bond 0.00374 ( 2559) covalent geometry : angle 0.46144 ( 3453) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.264 Fit side-chains REVERT: C 962 LEU cc_start: 0.8680 (tm) cc_final: 0.8440 (tt) REVERT: C 973 ILE cc_start: 0.9075 (mt) cc_final: 0.8807 (mt) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.5142 time to fit residues: 22.3791 Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.142648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.124515 restraints weight = 3566.140| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.21 r_work: 0.3941 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2559 Z= 0.139 Angle : 0.451 7.215 3453 Z= 0.239 Chirality : 0.038 0.156 435 Planarity : 0.002 0.013 453 Dihedral : 3.139 11.107 339 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.68 % Allowed : 18.18 % Favored : 80.13 % 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: 4.85 (0.45), residues: 327 helix: 4.09 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.05 (0.81), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.004 0.001 PHE A 927 ARG 0.002 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 232) hydrogen bonds : angle 2.88265 ( 696) covalent geometry : bond 0.00304 ( 2559) covalent geometry : angle 0.45089 ( 3453) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.298 Fit side-chains REVERT: C 962 LEU cc_start: 0.8667 (tm) cc_final: 0.8435 (tt) REVERT: C 973 ILE cc_start: 0.9054 (mt) cc_final: 0.8792 (mt) outliers start: 5 outliers final: 4 residues processed: 39 average time/residue: 0.4797 time to fit residues: 19.9943 Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 8.9990 chunk 11 optimal weight: 0.0970 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.141787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.123748 restraints weight = 3562.363| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.19 r_work: 0.3937 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 2559 Z= 0.143 Angle : 0.455 7.045 3453 Z= 0.248 Chirality : 0.039 0.193 435 Planarity : 0.002 0.013 453 Dihedral : 3.135 10.782 339 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.68 % Allowed : 18.18 % Favored : 80.13 % 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: 4.82 (0.45), residues: 327 helix: 4.08 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.08 (0.80), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.004 0.001 PHE B 970 ARG 0.003 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 232) hydrogen bonds : angle 2.93400 ( 696) covalent geometry : bond 0.00323 ( 2559) covalent geometry : angle 0.45516 ( 3453) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.287 Fit side-chains REVERT: C 962 LEU cc_start: 0.8662 (tm) cc_final: 0.8434 (tt) REVERT: C 973 ILE cc_start: 0.9050 (mt) cc_final: 0.8784 (mt) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.5075 time to fit residues: 22.1253 Evaluate side-chains 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN F1159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.142579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.124493 restraints weight = 3610.215| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.23 r_work: 0.3926 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 2559 Z= 0.152 Angle : 0.476 7.165 3453 Z= 0.255 Chirality : 0.039 0.183 435 Planarity : 0.002 0.016 453 Dihedral : 3.185 11.369 339 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 2.02 % Allowed : 17.85 % Favored : 80.13 % 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: 4.75 (0.45), residues: 327 helix: 4.03 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.12 (0.80), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.005 0.001 PHE B 970 ARG 0.003 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 232) hydrogen bonds : angle 2.95278 ( 696) covalent geometry : bond 0.00343 ( 2559) covalent geometry : angle 0.47618 ( 3453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1892.26 seconds wall clock time: 33 minutes 3.26 seconds (1983.26 seconds total)