Starting phenix.real_space_refine on Mon Feb 10 20:44:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzt_24777/02_2025/7rzt_24777.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzt_24777/02_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_24777/02_2025/7rzt_24777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzt_24777/02_2025/7rzt_24777.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzt_24777/02_2025/7rzt_24777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzt_24777/02_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-5592/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: 1.72, per 1000 atoms: 0.70 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: 0.63 Conformation dependent library (CDL) restraints added in 301.5 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: 0.21 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: 0.67 Time building geometry restraints manager: 0.69 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: 0.680 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.590 Find NCS groups from input model: 0.050 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:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- 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 : 0.253 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: 0.3369 time to fit residues: 7.2096 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 : 0.255 ------------------------------------------------------------------------------- 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: 0.7980 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 = 0.144953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.125529 restraints weight = 2904.359| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.08 r_work: 0.3822 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 : 0.280 Fit side-chains REVERT: A 974 SER cc_start: 0.8275 (p) cc_final: 0.7553 (p) REVERT: A 978 ASN cc_start: 0.8301 (m-40) cc_final: 0.8008 (m110) REVERT: C 979 ASP cc_start: 0.7405 (m-30) cc_final: 0.7182 (m-30) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.3713 time to fit residues: 6.7373 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 : 0.275 ------------------------------------------------------------------------------- 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: 0.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 8 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.149985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.132163 restraints weight = 2917.898| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.99 r_work: 0.3832 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2454 Z= 0.164 Angle : 0.245 1.915 3309 Z= 0.144 Chirality : 0.031 0.101 417 Planarity : 0.001 0.006 435 Dihedral : 2.784 8.669 324 Min Nonbonded Distance : 2.618 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: 5.77 (0.43), residues: 312 helix: 4.94 (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 0.009 0.001 PHE A 940 ARG 0.001 0.000 ARG B 983 *********************** 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 : 0.265 Fit side-chains REVERT: A 974 SER cc_start: 0.8303 (p) cc_final: 0.7633 (p) REVERT: A 978 ASN cc_start: 0.8336 (m-40) cc_final: 0.8098 (m110) REVERT: C 979 ASP cc_start: 0.7601 (m-30) cc_final: 0.7383 (m-30) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.3967 time to fit residues: 7.2141 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 : 0.287 ------------------------------------------------------------------------------- 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: 0.9980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 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 = 0.4242 r_free = 0.4242 target = 0.144601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.125373 restraints weight = 2911.141| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.06 r_work: 0.3804 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1288 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 : 0.276 2.104 3309 Z= 0.158 Chirality : 0.033 0.100 417 Planarity : 0.001 0.005 435 Dihedral : 2.892 9.265 324 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.04 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: 5.74 (0.43), residues: 312 helix: 4.91 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -1.22 (0.69), 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 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 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.265 Fit side-chains REVERT: A 974 SER cc_start: 0.8266 (p) cc_final: 0.7513 (p) REVERT: A 978 ASN cc_start: 0.8236 (m-40) cc_final: 0.7953 (m110) REVERT: C 979 ASP cc_start: 0.7476 (m-30) cc_final: 0.7246 (m-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.3484 time to fit residues: 6.6907 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 : 0.258 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4284 r_free = 0.4284 target = 0.149091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.131177 restraints weight = 2996.863| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.03 r_work: 0.3819 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2454 Z= 0.220 Angle : 0.267 2.074 3309 Z= 0.154 Chirality : 0.032 0.100 417 Planarity : 0.001 0.005 435 Dihedral : 2.841 9.050 324 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.04 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: 5.87 (0.43), residues: 312 helix: 4.98 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -1.08 (0.72), 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 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 : 0.281 Fit side-chains REVERT: A 974 SER cc_start: 0.8281 (p) cc_final: 0.7585 (p) REVERT: A 978 ASN cc_start: 0.8299 (m-40) cc_final: 0.8063 (m110) REVERT: C 979 ASP cc_start: 0.7632 (m-30) cc_final: 0.7395 (m-30) outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 0.3627 time to fit residues: 7.0125 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 : 0.252 ------------------------------------------------------------------------------- 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: 0.6980 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 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 = 0.148948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.131047 restraints weight = 2937.329| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.00 r_work: 0.3818 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1444 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= 0.213 Angle : 0.267 2.342 3309 Z= 0.154 Chirality : 0.032 0.102 417 Planarity : 0.001 0.005 435 Dihedral : 2.837 9.104 324 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.04 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: 5.93 (0.43), residues: 312 helix: 5.00 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -0.97 (0.74), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 940 ARG 0.000 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 : 0.276 Fit side-chains REVERT: A 978 ASN cc_start: 0.8267 (m-40) cc_final: 0.8040 (m110) REVERT: C 979 ASP cc_start: 0.7608 (m-30) cc_final: 0.7380 (m-30) outliers start: 1 outliers final: 0 residues processed: 16 average time/residue: 0.3756 time to fit residues: 6.7861 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 : 0.254 ------------------------------------------------------------------------------- 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: 0.7980 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.149076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.130987 restraints weight = 3013.861| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.04 r_work: 0.3816 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1488 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= 0.187 Angle : 0.255 2.286 3309 Z= 0.148 Chirality : 0.032 0.101 417 Planarity : 0.001 0.005 435 Dihedral : 2.772 8.815 324 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 6.08 (0.42), residues: 312 helix: 5.12 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -0.96 (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 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 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.260 Fit side-chains REVERT: A 978 ASN cc_start: 0.8315 (m-40) cc_final: 0.8076 (m110) REVERT: C 979 ASP cc_start: 0.7657 (m-30) cc_final: 0.7420 (m-30) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.3689 time to fit residues: 6.6736 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 : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 975 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.0970 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.149970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.131883 restraints weight = 2947.104| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.02 r_work: 0.3833 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2454 Z= 0.152 Angle : 0.239 2.263 3309 Z= 0.141 Chirality : 0.031 0.101 417 Planarity : 0.001 0.004 435 Dihedral : 2.687 8.588 324 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 5.32 % 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: 6.31 (0.42), residues: 312 helix: 5.27 (0.23), residues: 246 sheet: None (None), residues: 0 loop : -0.85 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 940 ARG 0.000 0.000 ARG B 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 18 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.256 Fit side-chains REVERT: C 979 ASP cc_start: 0.7576 (m-30) cc_final: 0.7345 (m-30) outliers start: 2 outliers final: 1 residues processed: 16 average time/residue: 0.3849 time to fit residues: 6.9293 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 : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 975 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 0.0970 chunk 11 optimal weight: 0.1980 chunk 21 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.149498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.131798 restraints weight = 2892.331| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.97 r_work: 0.3832 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2454 Z= 0.161 Angle : 0.261 3.207 3309 Z= 0.155 Chirality : 0.032 0.102 417 Planarity : 0.001 0.005 435 Dihedral : 2.689 8.540 324 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % 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: 6.27 (0.42), residues: 312 helix: 5.23 (0.23), residues: 246 sheet: None (None), residues: 0 loop : -0.80 (0.73), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 940 ARG 0.000 0.000 ARG C 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 : 0.338 Fit side-chains REVERT: C 979 ASP cc_start: 0.7597 (m-30) cc_final: 0.7361 (m-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3695 time to fit residues: 6.6904 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 : 0.253 ------------------------------------------------------------------------------- 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: 0.3980 chunk 1 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 2 optimal weight: 0.0770 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.2938 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.149853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.132051 restraints weight = 2925.929| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.00 r_work: 0.3838 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2454 Z= 0.129 Angle : 0.245 3.429 3309 Z= 0.149 Chirality : 0.031 0.103 417 Planarity : 0.001 0.005 435 Dihedral : 2.602 8.470 324 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 6.44 (0.42), residues: 312 helix: 5.35 (0.23), residues: 246 sheet: None (None), residues: 0 loop : -0.71 (0.74), 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 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 : 0.268 Fit side-chains REVERT: C 979 ASP cc_start: 0.7566 (m-30) cc_final: 0.7351 (m-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3763 time to fit residues: 6.7877 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 : 0.285 ------------------------------------------------------------------------------- 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: 0.7980 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.147966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.129868 restraints weight = 2967.335| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.04 r_work: 0.3806 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1618 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= 0.268 Angle : 0.307 3.395 3309 Z= 0.178 Chirality : 0.034 0.101 417 Planarity : 0.001 0.005 435 Dihedral : 2.857 8.877 324 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % 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: 5.95 (0.42), residues: 312 helix: 4.97 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -0.77 (0.73), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE A 940 ARG 0.001 0.000 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1940.12 seconds wall clock time: 35 minutes 0.90 seconds (2100.90 seconds total)