Sun 23 Dec 22:23:02 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2o3l-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o3l-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o3l-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-3.2-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-3.2-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:12 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-3.2-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 149 and 0 Target number of residues in the AU: 149 Target solvent content: 0.6325 Checking the provided sequence file Detected sequence length: 85 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 170 Adjusted target solvent content: 0.58 Input MTZ file: 2o3l-3.2-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 154 Cell parameters: 61.138 61.138 101.686 90.000 90.000 120.000 Input sequence file: 2o3l-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1360 target number of atoms Had to go as low as 0.85 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 52.947 3.201 Wilson plot Bfac: 67.07 3896 reflections ( 99.82 % complete ) and 0 restraints for refining 1515 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Starting model: R = 0.3466 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2865 (Rfree = 0.000) for 1515 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 2.86 Search for helices and strands: 0 residues in 0 chains, 1548 seeds are put forward NCS extension: 0 residues added, 1548 seeds are put forward Round 1: 96 peptides, 16 chains. Longest chain 14 peptides. Score 0.425 Round 2: 114 peptides, 18 chains. Longest chain 15 peptides. Score 0.488 Round 3: 104 peptides, 13 chains. Longest chain 16 peptides. Score 0.563 Round 4: 109 peptides, 13 chains. Longest chain 18 peptides. Score 0.592 Round 5: 108 peptides, 15 chains. Longest chain 13 peptides. Score 0.533 Taking the results from Round 4 Chains 13, Residues 96, Estimated correctness of the model 38.8 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 2637 restraints for refining 1241 atoms. 2215 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2733 (Rfree = 0.000) for 1241 atoms. Found 10 (11 requested) and removed 6 (5 requested) atoms. Cycle 2: After refmac, R = 0.2729 (Rfree = 0.000) for 1217 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 3: After refmac, R = 0.2421 (Rfree = 0.000) for 1215 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 4: After refmac, R = 0.2290 (Rfree = 0.000) for 1211 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. Cycle 5: After refmac, R = 0.2213 (Rfree = 0.000) for 1208 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 2.86 Search for helices and strands: 0 residues in 0 chains, 1283 seeds are put forward NCS extension: 0 residues added, 1283 seeds are put forward Round 1: 109 peptides, 14 chains. Longest chain 26 peptides. Score 0.566 Round 2: 123 peptides, 12 chains. Longest chain 19 peptides. Score 0.686 Round 3: 123 peptides, 16 chains. Longest chain 17 peptides. Score 0.594 Round 4: 123 peptides, 14 chains. Longest chain 17 peptides. Score 0.642 Round 5: 124 peptides, 12 chains. Longest chain 18 peptides. Score 0.690 Taking the results from Round 5 Chains 12, Residues 112, Estimated correctness of the model 63.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 2486 restraints for refining 1242 atoms. 1997 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2543 (Rfree = 0.000) for 1242 atoms. Found 8 (11 requested) and removed 20 (5 requested) atoms. Cycle 7: After refmac, R = 0.2307 (Rfree = 0.000) for 1223 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 8: After refmac, R = 0.2209 (Rfree = 0.000) for 1220 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 9: After refmac, R = 0.2175 (Rfree = 0.000) for 1216 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.2108 (Rfree = 0.000) for 1214 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 2.88 Search for helices and strands: 0 residues in 0 chains, 1269 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 1275 seeds are put forward Round 1: 107 peptides, 13 chains. Longest chain 15 peptides. Score 0.581 Round 2: 109 peptides, 12 chains. Longest chain 16 peptides. Score 0.617 Round 3: 112 peptides, 15 chains. Longest chain 17 peptides. Score 0.557 Round 4: 118 peptides, 13 chains. Longest chain 21 peptides. Score 0.640 Round 5: 115 peptides, 12 chains. Longest chain 21 peptides. Score 0.648 Taking the results from Round 5 Chains 13, Residues 103, Estimated correctness of the model 53.3 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 2366 restraints for refining 1242 atoms. 1875 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2691 (Rfree = 0.000) for 1242 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 12: After refmac, R = 0.2671 (Rfree = 0.000) for 1236 atoms. Found 10 (11 requested) and removed 6 (5 requested) atoms. Cycle 13: After refmac, R = 0.2685 (Rfree = 0.000) for 1228 atoms. Found 8 (11 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.2681 (Rfree = 0.000) for 1222 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.2620 (Rfree = 0.000) for 1220 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 2.88 Search for helices and strands: 0 residues in 0 chains, 1283 seeds are put forward NCS extension: 0 residues added, 1283 seeds are put forward Round 1: 107 peptides, 14 chains. Longest chain 23 peptides. Score 0.554 Round 2: 114 peptides, 13 chains. Longest chain 25 peptides. Score 0.619 Round 3: 115 peptides, 11 chains. Longest chain 24 peptides. Score 0.671 Round 4: 109 peptides, 12 chains. Longest chain 21 peptides. Score 0.617 Round 5: 127 peptides, 12 chains. Longest chain 29 peptides. Score 0.703 Taking the results from Round 5 Chains 13, Residues 115, Estimated correctness of the model 65.8 % 2 chains (12 residues) have been docked in sequence Building loops using Loopy2018 13 chains (115 residues) following loop building 2 chains (12 residues) in sequence following loop building ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 2475 restraints for refining 1242 atoms. 1995 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2625 (Rfree = 0.000) for 1242 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 17: After refmac, R = 0.2370 (Rfree = 0.000) for 1234 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.2670 (Rfree = 0.000) for 1228 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.2557 (Rfree = 0.000) for 1230 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.2105 (Rfree = 0.000) for 1223 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 2.84 Search for helices and strands: 0 residues in 0 chains, 1279 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 1293 seeds are put forward Round 1: 115 peptides, 16 chains. Longest chain 21 peptides. Score 0.549 Round 2: 127 peptides, 16 chains. Longest chain 17 peptides. Score 0.616 Round 3: 129 peptides, 14 chains. Longest chain 17 peptides. Score 0.670 Round 4: 118 peptides, 11 chains. Longest chain 28 peptides. Score 0.685 Round 5: 118 peptides, 13 chains. Longest chain 23 peptides. Score 0.640 Taking the results from Round 4 Chains 12, Residues 107, Estimated correctness of the model 61.9 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 2210 restraints for refining 1241 atoms. 1632 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2732 (Rfree = 0.000) for 1241 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 22: After refmac, R = 0.2769 (Rfree = 0.000) for 1228 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 23: After refmac, R = 0.2682 (Rfree = 0.000) for 1224 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 24: After refmac, R = 0.2557 (Rfree = 0.000) for 1218 atoms. Found 9 (9 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.2628 (Rfree = 0.000) for 1214 atoms. Found 9 (9 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 2.87 Search for helices and strands: 0 residues in 0 chains, 1287 seeds are put forward NCS extension: 0 residues added, 1287 seeds are put forward Round 1: 93 peptides, 14 chains. Longest chain 13 peptides. Score 0.465 Round 2: 112 peptides, 14 chains. Longest chain 15 peptides. Score 0.583 Round 3: 113 peptides, 12 chains. Longest chain 26 peptides. Score 0.638 Round 4: 109 peptides, 13 chains. Longest chain 16 peptides. Score 0.592 Round 5: 110 peptides, 11 chains. Longest chain 25 peptides. Score 0.646 Taking the results from Round 5 Chains 11, Residues 99, Estimated correctness of the model 52.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 2677 restraints for refining 1242 atoms. 2292 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2631 (Rfree = 0.000) for 1242 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 27: After refmac, R = 0.2208 (Rfree = 0.000) for 1235 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. Cycle 28: After refmac, R = 0.1998 (Rfree = 0.000) for 1226 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.1903 (Rfree = 0.000) for 1225 atoms. Found 4 (9 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.1860 (Rfree = 0.000) for 1222 atoms. Found 4 (9 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 2.88 Search for helices and strands: 0 residues in 0 chains, 1287 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 1311 seeds are put forward Round 1: 106 peptides, 18 chains. Longest chain 17 peptides. Score 0.434 Round 2: 121 peptides, 16 chains. Longest chain 17 peptides. Score 0.583 Round 3: 114 peptides, 15 chains. Longest chain 17 peptides. Score 0.569 Round 4: 114 peptides, 15 chains. Longest chain 18 peptides. Score 0.569 Round 5: 117 peptides, 16 chains. Longest chain 18 peptides. Score 0.560 Taking the results from Round 2 Chains 16, Residues 105, Estimated correctness of the model 36.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 2685 restraints for refining 1242 atoms. 2281 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2183 (Rfree = 0.000) for 1242 atoms. Found 9 (10 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.2029 (Rfree = 0.000) for 1241 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.2048 (Rfree = 0.000) for 1236 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.1941 (Rfree = 0.000) for 1230 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1910 (Rfree = 0.000) for 1225 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 2.85 Search for helices and strands: 0 residues in 0 chains, 1279 seeds are put forward NCS extension: 7 residues added (1 deleted due to clashes), 1286 seeds are put forward Round 1: 104 peptides, 17 chains. Longest chain 15 peptides. Score 0.450 Round 2: 107 peptides, 17 chains. Longest chain 13 peptides. Score 0.471 Round 3: 105 peptides, 17 chains. Longest chain 10 peptides. Score 0.457 Round 4: 107 peptides, 17 chains. Longest chain 11 peptides. Score 0.471 Round 5: 97 peptides, 16 chains. Longest chain 11 peptides. Score 0.432 Taking the results from Round 4 Chains 17, Residues 90, Estimated correctness of the model 1.6 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3896 reflections ( 99.82 % complete ) and 2657 restraints for refining 1242 atoms. 2283 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2673 (Rfree = 0.000) for 1242 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 37: After refmac, R = 0.2228 (Rfree = 0.000) for 1235 atoms. Found 9 (10 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.2033 (Rfree = 0.000) for 1231 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. Cycle 39: After refmac, R = 0.2045 (Rfree = 0.000) for 1228 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 40: After refmac, R = 0.2033 (Rfree = 0.000) for 1225 atoms. Found 2 (9 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 2.89 Search for helices and strands: 0 residues in 0 chains, 1285 seeds are put forward NCS extension: 0 residues added, 1285 seeds are put forward Round 1: 108 peptides, 18 chains. Longest chain 22 peptides. Score 0.448 Round 2: 111 peptides, 18 chains. Longest chain 16 peptides. Score 0.468 Round 3: 107 peptides, 18 chains. Longest chain 16 peptides. Score 0.441 Round 4: 110 peptides, 17 chains. Longest chain 16 peptides. Score 0.490 Round 5: 107 peptides, 17 chains. Longest chain 14 peptides. Score 0.471 Taking the results from Round 4 Chains 17, Residues 93, Estimated correctness of the model 8.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 2629 restraints for refining 1242 atoms. 2274 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2286 (Rfree = 0.000) for 1242 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 42: After refmac, R = 0.2359 (Rfree = 0.000) for 1241 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.2236 (Rfree = 0.000) for 1244 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. Cycle 44: After refmac, R = 0.2488 (Rfree = 0.000) for 1240 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 45: After refmac, R = 0.2209 (Rfree = 0.000) for 1237 atoms. Found 8 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 2.86 Search for helices and strands: 0 residues in 0 chains, 1307 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 1331 seeds are put forward Round 1: 72 peptides, 12 chains. Longest chain 11 peptides. Score 0.376 Round 2: 83 peptides, 14 chains. Longest chain 11 peptides. Score 0.393 Round 3: 91 peptides, 12 chains. Longest chain 16 peptides. Score 0.511 Round 4: 93 peptides, 11 chains. Longest chain 17 peptides. Score 0.552 Round 5: 90 peptides, 12 chains. Longest chain 20 peptides. Score 0.504 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 82, Estimated correctness of the model 27.4 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2o3l-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3896 reflections ( 99.82 % complete ) and 2607 restraints for refining 1242 atoms. 2246 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2895 (Rfree = 0.000) for 1242 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.3056 (Rfree = 0.000) for 1233 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2675 (Rfree = 0.000) for 1221 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2943 (Rfree = 0.000) for 1214 atoms. TimeTaking 28.4