null Sun 23 Dec 22:23:05 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 2it9-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2it9-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2it9-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2it9-3.8-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/2it9-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2it9-3.8-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 22:23:15 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/2it9-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2it9-3.8-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 383 and 0 Target number of residues in the AU: 383 Target solvent content: 0.6555 Checking the provided sequence file Detected sequence length: 127 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 508 Adjusted target solvent content: 0.54 Input MTZ file: 2it9-3.8-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: 19 Cell parameters: 59.723 81.014 124.347 90.000 90.000 90.000 Input sequence file: 2it9-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4064 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: 67.879 3.800 Wilson plot Bfac: 81.37 6215 reflections ( 98.15 % complete ) and 0 restraints for refining 4535 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3807 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3498 (Rfree = 0.000) for 4535 atoms. Found 24 (24 requested) and removed 49 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.42 Search for helices and strands: 0 residues in 0 chains, 4603 seeds are put forward NCS extension: 0 residues added, 4603 seeds are put forward Round 1: 189 peptides, 39 chains. Longest chain 9 peptides. Score 0.274 Round 2: 219 peptides, 37 chains. Longest chain 12 peptides. Score 0.386 Round 3: 260 peptides, 43 chains. Longest chain 14 peptides. Score 0.426 Round 4: 260 peptides, 39 chains. Longest chain 15 peptides. Score 0.470 Round 5: 258 peptides, 37 chains. Longest chain 18 peptides. Score 0.487 Taking the results from Round 5 Chains 37, Residues 221, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8338 restraints for refining 3675 atoms. 7448 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2935 (Rfree = 0.000) for 3675 atoms. Found 15 (20 requested) and removed 25 (10 requested) atoms. Cycle 2: After refmac, R = 0.2715 (Rfree = 0.000) for 3620 atoms. Found 12 (20 requested) and removed 21 (10 requested) atoms. Cycle 3: After refmac, R = 0.2645 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 4: After refmac, R = 0.2585 (Rfree = 0.000) for 3558 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 5: After refmac, R = 0.2179 (Rfree = 0.000) for 3552 atoms. Found 6 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 3652 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3677 seeds are put forward Round 1: 205 peptides, 39 chains. Longest chain 14 peptides. Score 0.322 Round 2: 229 peptides, 38 chains. Longest chain 13 peptides. Score 0.402 Round 3: 247 peptides, 38 chains. Longest chain 14 peptides. Score 0.449 Round 4: 240 peptides, 38 chains. Longest chain 15 peptides. Score 0.431 Round 5: 229 peptides, 37 chains. Longest chain 16 peptides. Score 0.413 Taking the results from Round 3 Chains 38, Residues 209, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8315 restraints for refining 3608 atoms. 7517 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2534 (Rfree = 0.000) for 3608 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 7: After refmac, R = 0.2464 (Rfree = 0.000) for 3568 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 8: After refmac, R = 0.2267 (Rfree = 0.000) for 3543 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 9: After refmac, R = 0.2119 (Rfree = 0.000) for 3536 atoms. Found 17 (19 requested) and removed 14 (9 requested) atoms. Cycle 10: After refmac, R = 0.1746 (Rfree = 0.000) for 3530 atoms. Found 8 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 3666 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3686 seeds are put forward Round 1: 202 peptides, 39 chains. Longest chain 12 peptides. Score 0.313 Round 2: 224 peptides, 38 chains. Longest chain 11 peptides. Score 0.388 Round 3: 234 peptides, 34 chains. Longest chain 17 peptides. Score 0.461 Round 4: 238 peptides, 38 chains. Longest chain 15 peptides. Score 0.425 Round 5: 251 peptides, 38 chains. Longest chain 12 peptides. Score 0.459 Taking the results from Round 3 Chains 37, Residues 200, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8217 restraints for refining 3676 atoms. 7380 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2505 (Rfree = 0.000) for 3676 atoms. Found 20 (20 requested) and removed 34 (10 requested) atoms. Cycle 12: After refmac, R = 0.2216 (Rfree = 0.000) for 3620 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 13: After refmac, R = 0.2015 (Rfree = 0.000) for 3605 atoms. Found 16 (19 requested) and removed 22 (9 requested) atoms. Cycle 14: After refmac, R = 0.2112 (Rfree = 0.000) for 3590 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 15: After refmac, R = 0.2147 (Rfree = 0.000) for 3590 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 3700 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3713 seeds are put forward Round 1: 206 peptides, 37 chains. Longest chain 13 peptides. Score 0.350 Round 2: 234 peptides, 39 chains. Longest chain 13 peptides. Score 0.403 Round 3: 243 peptides, 36 chains. Longest chain 18 peptides. Score 0.461 Round 4: 265 peptides, 36 chains. Longest chain 19 peptides. Score 0.514 Round 5: 252 peptides, 38 chains. Longest chain 14 peptides. Score 0.461 Taking the results from Round 4 Chains 36, Residues 229, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8098 restraints for refining 3675 atoms. 7218 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2455 (Rfree = 0.000) for 3675 atoms. Found 15 (20 requested) and removed 20 (10 requested) atoms. Cycle 17: After refmac, R = 0.2276 (Rfree = 0.000) for 3649 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 18: After refmac, R = 0.2212 (Rfree = 0.000) for 3626 atoms. Found 19 (20 requested) and removed 19 (10 requested) atoms. Cycle 19: After refmac, R = 0.2088 (Rfree = 0.000) for 3614 atoms. Found 18 (19 requested) and removed 17 (9 requested) atoms. Cycle 20: After refmac, R = 0.1768 (Rfree = 0.000) for 3603 atoms. Found 8 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 3732 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3753 seeds are put forward Round 1: 209 peptides, 41 chains. Longest chain 10 peptides. Score 0.309 Round 2: 219 peptides, 39 chains. Longest chain 13 peptides. Score 0.362 Round 3: 227 peptides, 32 chains. Longest chain 20 peptides. Score 0.466 Round 4: 212 peptides, 31 chains. Longest chain 17 peptides. Score 0.439 Round 5: 225 peptides, 34 chains. Longest chain 21 peptides. Score 0.438 Taking the results from Round 3 Chains 32, Residues 195, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8377 restraints for refining 3675 atoms. 7629 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2292 (Rfree = 0.000) for 3675 atoms. Found 17 (20 requested) and removed 18 (10 requested) atoms. Cycle 22: After refmac, R = 0.2186 (Rfree = 0.000) for 3654 atoms. Found 19 (20 requested) and removed 21 (10 requested) atoms. Cycle 23: After refmac, R = 0.1773 (Rfree = 0.000) for 3640 atoms. Found 7 (20 requested) and removed 12 (10 requested) atoms. Cycle 24: After refmac, R = 0.1736 (Rfree = 0.000) for 3627 atoms. Found 7 (19 requested) and removed 13 (9 requested) atoms. Cycle 25: After refmac, R = 0.1652 (Rfree = 0.000) for 3617 atoms. Found 7 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 3712 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3734 seeds are put forward Round 1: 208 peptides, 40 chains. Longest chain 11 peptides. Score 0.318 Round 2: 215 peptides, 35 chains. Longest chain 13 peptides. Score 0.399 Round 3: 229 peptides, 37 chains. Longest chain 14 peptides. Score 0.413 Round 4: 231 peptides, 36 chains. Longest chain 12 peptides. Score 0.430 Round 5: 242 peptides, 37 chains. Longest chain 14 peptides. Score 0.447 Taking the results from Round 5 Chains 37, Residues 205, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8313 restraints for refining 3676 atoms. 7530 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2268 (Rfree = 0.000) for 3676 atoms. Found 15 (20 requested) and removed 22 (10 requested) atoms. Cycle 27: After refmac, R = 0.2181 (Rfree = 0.000) for 3654 atoms. Found 13 (20 requested) and removed 17 (10 requested) atoms. Cycle 28: After refmac, R = 0.2106 (Rfree = 0.000) for 3640 atoms. Found 18 (20 requested) and removed 20 (10 requested) atoms. Cycle 29: After refmac, R = 0.2053 (Rfree = 0.000) for 3626 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 30: After refmac, R = 0.1615 (Rfree = 0.000) for 3621 atoms. Found 6 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 3729 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3747 seeds are put forward Round 1: 178 peptides, 35 chains. Longest chain 11 peptides. Score 0.292 Round 2: 218 peptides, 38 chains. Longest chain 11 peptides. Score 0.371 Round 3: 219 peptides, 38 chains. Longest chain 12 peptides. Score 0.374 Round 4: 227 peptides, 40 chains. Longest chain 15 peptides. Score 0.372 Round 5: 210 peptides, 35 chains. Longest chain 10 peptides. Score 0.385 Taking the results from Round 5 Chains 35, Residues 175, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8323 restraints for refining 3676 atoms. 7634 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2174 (Rfree = 0.000) for 3676 atoms. Found 11 (20 requested) and removed 16 (10 requested) atoms. Cycle 32: After refmac, R = 0.2053 (Rfree = 0.000) for 3654 atoms. Found 19 (20 requested) and removed 16 (10 requested) atoms. Cycle 33: After refmac, R = 0.1881 (Rfree = 0.000) for 3645 atoms. Found 16 (20 requested) and removed 17 (10 requested) atoms. Cycle 34: After refmac, R = 0.1947 (Rfree = 0.000) for 3642 atoms. Found 16 (20 requested) and removed 15 (10 requested) atoms. Cycle 35: After refmac, R = 0.1834 (Rfree = 0.000) for 3634 atoms. Found 15 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 3724 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3736 seeds are put forward Round 1: 157 peptides, 35 chains. Longest chain 6 peptides. Score 0.225 Round 2: 188 peptides, 35 chains. Longest chain 11 peptides. Score 0.322 Round 3: 189 peptides, 33 chains. Longest chain 11 peptides. Score 0.351 Round 4: 205 peptides, 37 chains. Longest chain 9 peptides. Score 0.347 Round 5: 211 peptides, 36 chains. Longest chain 13 peptides. Score 0.376 Taking the results from Round 5 Chains 36, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8306 restraints for refining 3675 atoms. 7642 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1900 (Rfree = 0.000) for 3675 atoms. Found 8 (20 requested) and removed 18 (10 requested) atoms. Cycle 37: After refmac, R = 0.1736 (Rfree = 0.000) for 3652 atoms. Found 4 (20 requested) and removed 14 (10 requested) atoms. Cycle 38: After refmac, R = 0.1857 (Rfree = 0.000) for 3636 atoms. Found 12 (20 requested) and removed 15 (10 requested) atoms. Cycle 39: After refmac, R = 0.1850 (Rfree = 0.000) for 3630 atoms. Found 19 (19 requested) and removed 10 (9 requested) atoms. Cycle 40: After refmac, R = 0.1833 (Rfree = 0.000) for 3629 atoms. Found 13 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 3726 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3742 seeds are put forward Round 1: 149 peptides, 33 chains. Longest chain 7 peptides. Score 0.226 Round 2: 183 peptides, 37 chains. Longest chain 8 peptides. Score 0.281 Round 3: 174 peptides, 34 chains. Longest chain 8 peptides. Score 0.293 Round 4: 168 peptides, 31 chains. Longest chain 8 peptides. Score 0.314 Round 5: 175 peptides, 31 chains. Longest chain 13 peptides. Score 0.335 Taking the results from Round 5 Chains 31, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8593 restraints for refining 3676 atoms. 8048 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2260 (Rfree = 0.000) for 3676 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 42: After refmac, R = 0.2089 (Rfree = 0.000) for 3668 atoms. Found 18 (20 requested) and removed 21 (10 requested) atoms. Cycle 43: After refmac, R = 0.1983 (Rfree = 0.000) for 3655 atoms. Found 18 (20 requested) and removed 21 (10 requested) atoms. Cycle 44: After refmac, R = 0.2053 (Rfree = 0.000) for 3646 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 45: After refmac, R = 0.1908 (Rfree = 0.000) for 3645 atoms. Found 15 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 3746 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3758 seeds are put forward Round 1: 127 peptides, 29 chains. Longest chain 6 peptides. Score 0.207 Round 2: 169 peptides, 35 chains. Longest chain 7 peptides. Score 0.264 Round 3: 161 peptides, 30 chains. Longest chain 16 peptides. Score 0.306 Round 4: 140 peptides, 29 chains. Longest chain 8 peptides. Score 0.252 Round 5: 152 peptides, 28 chains. Longest chain 10 peptides. Score 0.305 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 131, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2it9-3_warpNtrace.pdb as input Building loops using Loopy2018 30 chains (131 residues) following loop building 3 chains (14 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6215 reflections ( 98.15 % complete ) and 8267 restraints for refining 3676 atoms. 7718 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2097 (Rfree = 0.000) for 3676 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2005 (Rfree = 0.000) for 3653 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1920 (Rfree = 0.000) for 3642 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1967 (Rfree = 0.000) for 3628 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:20:05 GMT 2018 Job finished. TimeTaking 57.02 Used memory is bytes: 20551720