Starting phenix.real_space_refine on Wed Mar 5 15:40:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzt_24777/03_2025/7rzt_24777.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzt_24777/03_2025/7rzt_24777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rzt_24777/03_2025/7rzt_24777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzt_24777/03_2025/7rzt_24777.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzt_24777/03_2025/7rzt_24777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzt_24777/03_2025/7rzt_24777.cif" } resolution = 2.35 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= 0.018 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 1518 2.51 5 N 426 2.21 5 O 507 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-5624/modules/chem_data/mon_lib" Total number of atoms: 2451 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "E" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Restraints were copied for chains: C, B, D, F Time building chain proxies: 1.79, per 1000 atoms: 0.73 Number of scatterers: 2451 At special positions: 0 Unit cell: (48.975, 42.445, 116.724, 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 507 8.00 N 426 7.00 C 1518 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: 0.61 Conformation dependent library (CDL) restraints added in 346.0 milliseconds 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 618 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 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 Processing helix chain 'E' and resid 1179 through 1193 Processing helix 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 235 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: 0.66 Time building geometry restraints manager: 0.73 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: 465 1.29 - 1.35: 399 1.35 - 1.42: 61 1.42 - 1.48: 365 1.48 - 1.54: 1164 Bond restraints: 2454 Sorted by residual: bond pdb=" C ILE F1179 " pdb=" O ILE F1179 " ideal model delta sigma weight residual 1.236 1.227 0.010 1.19e-02 7.06e+03 6.50e-01 bond pdb=" N VAL D1176 " pdb=" CA VAL D1176 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.15e-02 7.56e+03 5.99e-01 bond pdb=" N VAL F1176 " pdb=" CA VAL F1176 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.15e-02 7.56e+03 5.98e-01 bond pdb=" N VAL E1176 " pdb=" CA VAL E1176 " ideal model delta sigma weight residual 1.457 1.448 0.008 1.15e-02 7.56e+03 5.44e-01 bond pdb=" C ILE E1179 " pdb=" O ILE E1179 " ideal model delta sigma weight residual 1.236 1.228 0.009 1.19e-02 7.06e+03 5.18e-01 ... (remaining 2449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.46: 2912 0.46 - 0.91: 344 0.91 - 1.37: 39 1.37 - 1.82: 11 1.82 - 2.28: 3 Bond angle restraints: 3309 Sorted by residual: angle pdb=" N ILE D1169 " pdb=" CA ILE D1169 " pdb=" C ILE D1169 " ideal model delta sigma weight residual 109.34 111.62 -2.28 2.08e+00 2.31e-01 1.20e+00 angle pdb=" N ILE E1169 " pdb=" CA ILE E1169 " pdb=" C ILE E1169 " ideal model delta sigma weight residual 109.34 111.62 -2.28 2.08e+00 2.31e-01 1.20e+00 angle pdb=" N ILE F1169 " pdb=" CA ILE F1169 " pdb=" C ILE F1169 " ideal model delta sigma weight residual 109.34 111.61 -2.27 2.08e+00 2.31e-01 1.19e+00 angle pdb=" CA ILE F1169 " pdb=" C ILE F1169 " pdb=" N SER F1170 " ideal model delta sigma weight residual 116.60 117.95 -1.35 1.45e+00 4.76e-01 8.69e-01 angle pdb=" CA ILE E1169 " pdb=" C ILE E1169 " pdb=" N SER E1170 " ideal model delta sigma weight residual 116.60 117.95 -1.35 1.45e+00 4.76e-01 8.61e-01 ... (remaining 3304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 1386 17.87 - 35.74: 120 35.74 - 53.60: 9 53.60 - 71.47: 9 71.47 - 89.34: 6 Dihedral angle restraints: 1530 sinusoidal: 594 harmonic: 936 Sorted by residual: dihedral pdb=" N LEU A 984 " pdb=" CA LEU A 984 " pdb=" CB LEU A 984 " pdb=" CG LEU A 984 " ideal model delta sinusoidal sigma weight residual -60.00 -94.67 34.67 3 1.50e+01 4.44e-03 5.89e+00 dihedral pdb=" N LEU C 984 " pdb=" CA LEU C 984 " pdb=" CB LEU C 984 " pdb=" CG LEU C 984 " ideal model delta sinusoidal sigma weight residual -60.00 -94.64 34.64 3 1.50e+01 4.44e-03 5.88e+00 dihedral pdb=" CB GLU A 918 " pdb=" CG GLU A 918 " pdb=" CD GLU A 918 " pdb=" OE1 GLU A 918 " ideal model delta sinusoidal sigma weight residual 0.00 63.30 -63.30 1 3.00e+01 1.11e-03 5.87e+00 ... (remaining 1527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 179 0.020 - 0.040: 165 0.040 - 0.060: 54 0.060 - 0.080: 10 0.080 - 0.100: 9 Chirality restraints: 417 Sorted by residual: chirality pdb=" CA ILE F1172 " pdb=" N ILE F1172 " pdb=" C ILE F1172 " pdb=" CB ILE F1172 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.52e-01 chirality pdb=" CA ILE E1172 " pdb=" N ILE E1172 " pdb=" C ILE E1172 " pdb=" CB ILE E1172 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.51e-01 chirality pdb=" CA ILE D1172 " pdb=" N ILE D1172 " pdb=" C ILE D1172 " pdb=" CB ILE D1172 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.48e-01 ... (remaining 414 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 952 " 0.003 2.00e-02 2.50e+03 6.56e-03 4.31e-01 pdb=" C VAL C 952 " -0.011 2.00e-02 2.50e+03 pdb=" O VAL C 952 " 0.004 2.00e-02 2.50e+03 pdb=" N ASN C 953 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 952 " 0.003 2.00e-02 2.50e+03 6.38e-03 4.08e-01 pdb=" C VAL B 952 " -0.011 2.00e-02 2.50e+03 pdb=" O VAL B 952 " 0.004 2.00e-02 2.50e+03 pdb=" N ASN B 953 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 952 " -0.003 2.00e-02 2.50e+03 6.37e-03 4.06e-01 pdb=" C VAL A 952 " 0.011 2.00e-02 2.50e+03 pdb=" O VAL A 952 " -0.004 2.00e-02 2.50e+03 pdb=" N ASN A 953 " -0.004 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 874 2.89 - 3.39: 2738 3.39 - 3.90: 4194 3.90 - 4.40: 4448 4.40 - 4.90: 7655 Nonbonded interactions: 19909 Sorted by model distance: nonbonded pdb=" NE2 GLN A 935 " pdb=" O ALA D1190 " model vdw 2.388 3.120 nonbonded pdb=" NE2 GLN B 935 " pdb=" O ALA E1190 " model vdw 2.388 3.120 nonbonded pdb=" NE2 GLN C 935 " pdb=" O ALA F1190 " model vdw 2.389 3.120 nonbonded pdb=" O GLY C 971 " pdb=" OG SER C 974 " model vdw 2.458 3.040 nonbonded pdb=" O GLY B 971 " pdb=" OG SER B 974 " model vdw 2.459 3.040 ... (remaining 19904 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: 0.720 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.820 Find NCS groups from input model: 0.060 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.005 0.022 2454 Z= 0.325 Angle : 0.319 2.279 3309 Z= 0.199 Chirality : 0.032 0.100 417 Planarity : 0.002 0.007 435 Dihedral : 14.893 89.342 912 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: 2.81 (0.41), residues: 312 helix: 2.81 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -2.14 (0.61), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE C 970 ARG 0.001 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.279 Fit side-chains REVERT: A 974 SER cc_start: 0.8081 (p) cc_final: 0.7389 (p) REVERT: A 978 ASN cc_start: 0.8215 (m-40) cc_final: 0.7828 (m110) REVERT: C 979 ASP cc_start: 0.7179 (m-30) cc_final: 0.6959 (m-30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.3534 time to fit residues: 7.5813 Evaluate side-chains 19 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN E1173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.144975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.125610 restraints weight = 2904.289| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.09 r_work: 0.3812 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2454 Z= 0.211 Angle : 0.287 2.463 3309 Z= 0.165 Chirality : 0.032 0.100 417 Planarity : 0.002 0.009 435 Dihedral : 2.956 9.582 324 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 3.90 % Favored : 95.74 % 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: 4.97 (0.43), residues: 312 helix: 4.38 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -1.58 (0.64), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 940 ARG 0.001 0.000 ARG E1185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.264 Fit side-chains REVERT: A 974 SER cc_start: 0.8258 (p) cc_final: 0.7533 (p) REVERT: A 978 ASN cc_start: 0.8283 (m-40) cc_final: 0.7991 (m110) REVERT: C 979 ASP cc_start: 0.7402 (m-30) cc_final: 0.7179 (m-30) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.3434 time to fit residues: 6.2121 Evaluate side-chains 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 975 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 8 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.150218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.132435 restraints weight = 2916.540| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 1.98 r_work: 0.3833 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2454 Z= 0.150 Angle : 0.240 1.944 3309 Z= 0.142 Chirality : 0.031 0.101 417 Planarity : 0.001 0.006 435 Dihedral : 2.754 8.515 324 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 4.61 % Favored : 95.04 % 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: 5.83 (0.43), residues: 312 helix: 5.00 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -1.29 (0.68), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 940 ARG 0.001 0.000 ARG E1185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.246 Fit side-chains REVERT: A 974 SER cc_start: 0.8305 (p) cc_final: 0.7642 (p) REVERT: A 978 ASN cc_start: 0.8329 (m-40) cc_final: 0.8086 (m110) REVERT: C 979 ASP cc_start: 0.7588 (m-30) cc_final: 0.7376 (m-30) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.3347 time to fit residues: 6.0832 Evaluate side-chains 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 975 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.144949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.125430 restraints weight = 2908.683| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.10 r_work: 0.3804 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2454 Z= 0.231 Angle : 0.274 2.035 3309 Z= 0.158 Chirality : 0.033 0.100 417 Planarity : 0.001 0.005 435 Dihedral : 2.876 9.201 324 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % 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: 5.77 (0.43), residues: 312 helix: 4.94 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -1.23 (0.68), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE A 940 ARG 0.001 0.000 ARG E1185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.274 Fit side-chains REVERT: A 974 SER cc_start: 0.8256 (p) cc_final: 0.7511 (p) REVERT: A 978 ASN cc_start: 0.8225 (m-40) cc_final: 0.7941 (m110) REVERT: C 979 ASP cc_start: 0.7432 (m-30) cc_final: 0.7208 (m-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3671 time to fit residues: 6.6859 Evaluate side-chains 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.149715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.131802 restraints weight = 2992.527| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.01 r_work: 0.3822 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2454 Z= 0.187 Angle : 0.252 1.977 3309 Z= 0.147 Chirality : 0.032 0.100 417 Planarity : 0.001 0.005 435 Dihedral : 2.771 8.798 324 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 4.96 % Favored : 94.68 % 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: 6.01 (0.43), residues: 312 helix: 5.10 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -1.13 (0.71), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 940 ARG 0.001 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.269 Fit side-chains REVERT: A 974 SER cc_start: 0.8300 (p) cc_final: 0.7606 (p) REVERT: A 978 ASN cc_start: 0.8317 (m-40) cc_final: 0.8076 (m110) REVERT: C 979 ASP cc_start: 0.7625 (m-30) cc_final: 0.7400 (m-30) outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 0.3568 time to fit residues: 6.9080 Evaluate side-chains 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.148639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.130728 restraints weight = 2938.617| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.00 r_work: 0.3822 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2454 Z= 0.228 Angle : 0.272 2.227 3309 Z= 0.157 Chirality : 0.033 0.101 417 Planarity : 0.001 0.005 435 Dihedral : 2.866 9.283 324 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.35 % Allowed : 5.32 % Favored : 94.33 % 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: 5.85 (0.42), residues: 312 helix: 4.98 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -1.15 (0.70), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE A 940 ARG 0.001 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.269 Fit side-chains REVERT: A 978 ASN cc_start: 0.8292 (m-40) cc_final: 0.8058 (m110) REVERT: C 979 ASP cc_start: 0.7614 (m-30) cc_final: 0.7382 (m-30) outliers start: 1 outliers final: 0 residues processed: 16 average time/residue: 0.3633 time to fit residues: 6.6174 Evaluate side-chains 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.149521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.131589 restraints weight = 3017.643| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.02 r_work: 0.3825 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2454 Z= 0.174 Angle : 0.249 2.146 3309 Z= 0.145 Chirality : 0.032 0.100 417 Planarity : 0.001 0.005 435 Dihedral : 2.750 8.704 324 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % 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: 6.13 (0.42), residues: 312 helix: 5.18 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -1.04 (0.71), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 940 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.276 Fit side-chains REVERT: A 978 ASN cc_start: 0.8288 (m-40) cc_final: 0.8051 (m110) REVERT: C 979 ASP cc_start: 0.7608 (m-30) cc_final: 0.7377 (m-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3680 time to fit residues: 6.6702 Evaluate side-chains 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4284 r_free = 0.4284 target = 0.149043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.131100 restraints weight = 2959.893| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.01 r_work: 0.3825 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2454 Z= 0.193 Angle : 0.258 2.351 3309 Z= 0.150 Chirality : 0.032 0.101 417 Planarity : 0.001 0.005 435 Dihedral : 2.779 8.919 324 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.35 % Allowed : 5.32 % Favored : 94.33 % 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: 6.11 (0.42), residues: 312 helix: 5.13 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -0.94 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 940 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.250 Fit side-chains REVERT: A 978 ASN cc_start: 0.8302 (m-40) cc_final: 0.8061 (m110) REVERT: C 979 ASP cc_start: 0.7602 (m-30) cc_final: 0.7371 (m-30) outliers start: 1 outliers final: 0 residues processed: 16 average time/residue: 0.3497 time to fit residues: 6.3264 Evaluate side-chains 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.4286 r_free = 0.4286 target = 0.149064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.131234 restraints weight = 2884.848| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.99 r_work: 0.3830 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2454 Z= 0.179 Angle : 0.253 2.192 3309 Z= 0.147 Chirality : 0.032 0.101 417 Planarity : 0.001 0.005 435 Dihedral : 2.747 8.607 324 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % 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: 6.20 (0.42), residues: 312 helix: 5.19 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -0.87 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 940 ARG 0.001 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.267 Fit side-chains REVERT: A 978 ASN cc_start: 0.8294 (m-40) cc_final: 0.8050 (m110) REVERT: C 979 ASP cc_start: 0.7558 (m-30) cc_final: 0.7342 (m-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3720 time to fit residues: 6.7574 Evaluate side-chains 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 0.0870 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4286 r_free = 0.4286 target = 0.149280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.131317 restraints weight = 2936.585| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.01 r_work: 0.3821 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2454 Z= 0.207 Angle : 0.265 2.216 3309 Z= 0.153 Chirality : 0.032 0.101 417 Planarity : 0.001 0.005 435 Dihedral : 2.791 8.769 324 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % 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: 6.08 (0.42), residues: 312 helix: 5.10 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -0.88 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 940 ARG 0.001 0.000 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.272 Fit side-chains REVERT: A 978 ASN cc_start: 0.8311 (m-40) cc_final: 0.8077 (m110) REVERT: C 979 ASP cc_start: 0.7611 (m-30) cc_final: 0.7377 (m-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3595 time to fit residues: 6.5162 Evaluate side-chains 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 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 = 0.4283 r_free = 0.4283 target = 0.148742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.130813 restraints weight = 2971.016| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.01 r_work: 0.3815 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2454 Z= 0.214 Angle : 0.269 2.288 3309 Z= 0.155 Chirality : 0.032 0.101 417 Planarity : 0.001 0.005 435 Dihedral : 2.804 8.922 324 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % 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: 6.04 (0.42), residues: 312 helix: 5.07 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -0.86 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 940 ARG 0.001 0.000 ARG C 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.95 seconds wall clock time: 32 minutes 12.85 seconds (1932.85 seconds total)