null Sun 23 Dec 22:23:10 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 2ilb-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ilb-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ilb-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-4.0-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/2ilb-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-4.0-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 22:23:19 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/2ilb-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-4.0-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 67 and 0 Target number of residues in the AU: 67 Target solvent content: 0.6636 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 114 Adjusted target solvent content: 0.43 Input MTZ file: 2ilb-4.0-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: 5 Cell parameters: 48.900 72.000 32.740 90.000 110.754 90.000 Input sequence file: 2ilb-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 912 target number of atoms Had to go as low as 0.75 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 Loops will be built when appropriate and at the last cycle Resolution range: 38.600 4.000 Wilson plot Bfac: 86.96 923 reflections ( 99.57 % complete ) and 0 restraints for refining 1004 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3341 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2995 (Rfree = 0.000) for 1004 atoms. Found 4 (4 requested) and removed 14 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.81 4.18 Search for helices and strands: 0 residues in 0 chains, 997 seeds are put forward Round 1: 18 peptides, 4 chains. Longest chain 5 peptides. Score 0.212 Round 2: 27 peptides, 6 chains. Longest chain 6 peptides. Score 0.225 Round 3: 25 peptides, 5 chains. Longest chain 6 peptides. Score 0.266 Round 4: 25 peptides, 5 chains. Longest chain 6 peptides. Score 0.266 Round 5: 28 peptides, 6 chains. Longest chain 6 peptides. Score 0.244 Taking the results from Round 4 Chains 5, Residues 20, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 923 reflections ( 99.57 % complete ) and 1972 restraints for refining 801 atoms. 1897 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2920 (Rfree = 0.000) for 801 atoms. Found 2 (3 requested) and removed 3 (1 requested) atoms. Cycle 2: After refmac, R = 0.3041 (Rfree = 0.000) for 791 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 3: After refmac, R = 0.3109 (Rfree = 0.000) for 786 atoms. Found 3 (3 requested) and removed 20 (1 requested) atoms. Cycle 4: After refmac, R = 0.2885 (Rfree = 0.000) for 760 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 5: After refmac, R = 0.2919 (Rfree = 0.000) for 757 atoms. Found 2 (3 requested) and removed 43 (1 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 3.97 Search for helices and strands: 0 residues in 0 chains, 737 seeds are put forward Round 1: 24 peptides, 6 chains. Longest chain 4 peptides. Score 0.167 Round 2: 23 peptides, 5 chains. Longest chain 6 peptides. Score 0.228 Round 3: 27 peptides, 5 chains. Longest chain 9 peptides. Score 0.303 Round 4: 24 peptides, 5 chains. Longest chain 7 peptides. Score 0.248 Round 5: 30 peptides, 5 chains. Longest chain 9 peptides. Score 0.354 Taking the results from Round 5 Chains 5, Residues 25, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 923 reflections ( 99.57 % complete ) and 1383 restraints for refining 655 atoms. 1288 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2788 (Rfree = 0.000) for 655 atoms. Found 3 (3 requested) and removed 23 (1 requested) atoms. Cycle 7: After refmac, R = 0.2836 (Rfree = 0.000) for 628 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 8: After refmac, R = 0.2887 (Rfree = 0.000) for 626 atoms. Found 2 (2 requested) and removed 23 (1 requested) atoms. Cycle 9: After refmac, R = 0.2580 (Rfree = 0.000) for 604 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 10: After refmac, R = 0.2572 (Rfree = 0.000) for 603 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.69 4.05 Search for helices and strands: 0 residues in 0 chains, 627 seeds are put forward Round 1: 29 peptides, 7 chains. Longest chain 5 peptides. Score 0.186 Round 2: 40 peptides, 8 chains. Longest chain 7 peptides. Score 0.306 Round 3: 37 peptides, 7 chains. Longest chain 7 peptides. Score 0.326 Round 4: 36 peptides, 7 chains. Longest chain 8 peptides. Score 0.309 Round 5: 38 peptides, 7 chains. Longest chain 9 peptides. Score 0.342 Taking the results from Round 5 Chains 7, Residues 31, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 923 reflections ( 99.57 % complete ) and 1360 restraints for refining 643 atoms. 1227 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2682 (Rfree = 0.000) for 643 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 12: After refmac, R = 0.2587 (Rfree = 0.000) for 635 atoms. Found 3 (3 requested) and removed 30 (1 requested) atoms. Cycle 13: After refmac, R = 0.2373 (Rfree = 0.000) for 605 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 14: After refmac, R = 0.2700 (Rfree = 0.000) for 600 atoms. Found 2 (2 requested) and removed 19 (1 requested) atoms. Cycle 15: After refmac, R = 0.2224 (Rfree = 0.000) for 582 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 4.14 Search for helices and strands: 0 residues in 0 chains, 608 seeds are put forward Round 1: 18 peptides, 4 chains. Longest chain 5 peptides. Score 0.212 Round 2: 37 peptides, 8 chains. Longest chain 7 peptides. Score 0.256 Round 3: 25 peptides, 4 chains. Longest chain 10 peptides. Score 0.345 Round 4: 25 peptides, 5 chains. Longest chain 7 peptides. Score 0.266 Round 5: 27 peptides, 5 chains. Longest chain 7 peptides. Score 0.303 Taking the results from Round 3 Chains 4, Residues 21, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 923 reflections ( 99.57 % complete ) and 1227 restraints for refining 582 atoms. 1134 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2355 (Rfree = 0.000) for 582 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 17: After refmac, R = 0.2498 (Rfree = 0.000) for 578 atoms. Found 2 (2 requested) and removed 11 (1 requested) atoms. Cycle 18: After refmac, R = 0.2070 (Rfree = 0.000) for 567 atoms. Found 1 (2 requested) and removed 1 (1 requested) atoms. Cycle 19: After refmac, R = 0.2431 (Rfree = 0.000) for 564 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 20: After refmac, R = 0.2210 (Rfree = 0.000) for 564 atoms. Found 2 (2 requested) and removed 6 (1 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 4.11 Search for helices and strands: 0 residues in 0 chains, 580 seeds are put forward Round 1: 33 peptides, 7 chains. Longest chain 7 peptides. Score 0.258 Round 2: 34 peptides, 7 chains. Longest chain 8 peptides. Score 0.276 Round 3: 34 peptides, 7 chains. Longest chain 7 peptides. Score 0.276 Round 4: 39 peptides, 6 chains. Longest chain 11 peptides. Score 0.425 Round 5: 40 peptides, 6 chains. Longest chain 10 peptides. Score 0.440 Taking the results from Round 5 Chains 6, Residues 34, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 923 reflections ( 99.57 % complete ) and 1246 restraints for refining 593 atoms. 1116 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3320 (Rfree = 0.000) for 593 atoms. Found 2 (2 requested) and removed 8 (1 requested) atoms. Cycle 22: After refmac, R = 0.2774 (Rfree = 0.000) for 581 atoms. Found 2 (2 requested) and removed 7 (1 requested) atoms. Cycle 23: After refmac, R = 0.2285 (Rfree = 0.000) for 570 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 24: After refmac, R = 0.2289 (Rfree = 0.000) for 570 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 25: After refmac, R = 0.1992 (Rfree = 0.000) for 567 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 3.97 Search for helices and strands: 0 residues in 0 chains, 595 seeds are put forward Round 1: 29 peptides, 6 chains. Longest chain 6 peptides. Score 0.262 Round 2: 26 peptides, 5 chains. Longest chain 7 peptides. Score 0.285 Round 3: 29 peptides, 5 chains. Longest chain 8 peptides. Score 0.337 Round 4: 27 peptides, 5 chains. Longest chain 7 peptides. Score 0.303 Round 5: 25 peptides, 4 chains. Longest chain 7 peptides. Score 0.345 Taking the results from Round 5 Chains 4, Residues 21, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 923 reflections ( 99.57 % complete ) and 1148 restraints for refining 571 atoms. 1068 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2454 (Rfree = 0.000) for 571 atoms. Found 2 (2 requested) and removed 13 (1 requested) atoms. Cycle 27: After refmac, R = 0.2490 (Rfree = 0.000) for 557 atoms. Found 2 (2 requested) and removed 6 (1 requested) atoms. Cycle 28: After refmac, R = 0.2165 (Rfree = 0.000) for 552 atoms. Found 1 (2 requested) and removed 4 (1 requested) atoms. Cycle 29: After refmac, R = 0.2232 (Rfree = 0.000) for 546 atoms. Found 2 (2 requested) and removed 4 (1 requested) atoms. Cycle 30: After refmac, R = 0.2254 (Rfree = 0.000) for 543 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.81 Search for helices and strands: 0 residues in 0 chains, 562 seeds are put forward Round 1: 32 peptides, 7 chains. Longest chain 7 peptides. Score 0.241 Round 2: 33 peptides, 6 chains. Longest chain 7 peptides. Score 0.331 Round 3: 27 peptides, 5 chains. Longest chain 7 peptides. Score 0.303 Round 4: 33 peptides, 6 chains. Longest chain 8 peptides. Score 0.331 Round 5: 33 peptides, 6 chains. Longest chain 8 peptides. Score 0.331 Taking the results from Round 5 Chains 6, Residues 27, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 923 reflections ( 99.57 % complete ) and 1232 restraints for refining 588 atoms. 1130 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2475 (Rfree = 0.000) for 588 atoms. Found 2 (2 requested) and removed 7 (1 requested) atoms. Cycle 32: After refmac, R = 0.2464 (Rfree = 0.000) for 578 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 33: After refmac, R = 0.2068 (Rfree = 0.000) for 571 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 34: After refmac, R = 0.2449 (Rfree = 0.000) for 567 atoms. Found 2 (2 requested) and removed 4 (1 requested) atoms. Cycle 35: After refmac, R = 0.2097 (Rfree = 0.000) for 562 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 4.04 Search for helices and strands: 0 residues in 0 chains, 581 seeds are put forward Round 1: 27 peptides, 5 chains. Longest chain 7 peptides. Score 0.303 Round 2: 26 peptides, 5 chains. Longest chain 8 peptides. Score 0.285 Round 3: 24 peptides, 4 chains. Longest chain 8 peptides. Score 0.328 Round 4: 26 peptides, 4 chains. Longest chain 7 peptides. Score 0.362 Round 5: 29 peptides, 4 chains. Longest chain 8 peptides. Score 0.411 Taking the results from Round 5 Chains 4, Residues 25, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 923 reflections ( 99.57 % complete ) and 1088 restraints for refining 554 atoms. 992 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2961 (Rfree = 0.000) for 554 atoms. Found 2 (2 requested) and removed 9 (1 requested) atoms. Cycle 37: After refmac, R = 0.2171 (Rfree = 0.000) for 541 atoms. Found 2 (2 requested) and removed 4 (1 requested) atoms. Cycle 38: After refmac, R = 0.2758 (Rfree = 0.000) for 537 atoms. Found 2 (2 requested) and removed 25 (1 requested) atoms. Cycle 39: After refmac, R = 0.2327 (Rfree = 0.000) for 512 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 40: After refmac, R = 0.2796 (Rfree = 0.000) for 509 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 4.01 Search for helices and strands: 0 residues in 0 chains, 536 seeds are put forward Round 1: 14 peptides, 3 chains. Longest chain 6 peptides. Score 0.217 Round 2: 21 peptides, 3 chains. Longest chain 9 peptides. Score 0.357 Round 3: 17 peptides, 3 chains. Longest chain 8 peptides. Score 0.282 Round 4: 25 peptides, 4 chains. Longest chain 10 peptides. Score 0.345 Round 5: 26 peptides, 4 chains. Longest chain 11 peptides. Score 0.362 Taking the results from Round 5 Chains 4, Residues 22, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 923 reflections ( 99.57 % complete ) and 996 restraints for refining 497 atoms. 912 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2644 (Rfree = 0.000) for 497 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 42: After refmac, R = 0.2327 (Rfree = 0.000) for 487 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 43: After refmac, R = 0.2526 (Rfree = 0.000) for 487 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 44: After refmac, R = 0.2238 (Rfree = 0.000) for 479 atoms. Found 1 (2 requested) and removed 1 (1 requested) atoms. Cycle 45: After refmac, R = 0.2268 (Rfree = 0.000) for 475 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 4.04 Search for helices and strands: 0 residues in 0 chains, 490 seeds are put forward Round 1: 20 peptides, 4 chains. Longest chain 6 peptides. Score 0.253 Round 2: 25 peptides, 3 chains. Longest chain 10 peptides. Score 0.423 Round 3: 28 peptides, 5 chains. Longest chain 8 peptides. Score 0.320 Round 4: 26 peptides, 4 chains. Longest chain 9 peptides. Score 0.362 Round 5: 29 peptides, 4 chains. Longest chain 13 peptides. Score 0.411 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 22, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2ilb-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 923 reflections ( 99.57 % complete ) and 898 restraints for refining 455 atoms. 813 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2838 (Rfree = 0.000) for 455 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Cycle 47: After refmac, R = 0.3391 (Rfree = 0.000) for 450 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Cycle 48: After refmac, R = 0.2632 (Rfree = 0.000) for 446 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Cycle 49: After refmac, R = 0.2958 (Rfree = 0.000) for 442 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:42:31 GMT 2018 Job finished. TimeTaking 19.36 Used memory is bytes: 1010064