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 1vjz-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjz-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjz-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-3.6-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/1vjz-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-3.6-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/1vjz-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-3.6-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 308 and 0 Target number of residues in the AU: 308 Target solvent content: 0.6062 Checking the provided sequence file Detected sequence length: 341 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 341 Adjusted target solvent content: 0.56 Input MTZ file: 1vjz-3.6-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: 96 Cell parameters: 64.677 64.677 202.367 90.000 90.000 90.000 Input sequence file: 1vjz-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2728 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: 61.607 3.600 Wilson plot Bfac: 54.80 5446 reflections ( 99.91 % complete ) and 0 restraints for refining 3021 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3322 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3173 (Rfree = 0.000) for 3021 atoms. Found 19 (19 requested) and removed 40 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 2.93 Search for helices and strands: 0 residues in 0 chains, 3044 seeds are put forward Round 1: 156 peptides, 31 chains. Longest chain 9 peptides. Score 0.308 Round 2: 182 peptides, 31 chains. Longest chain 11 peptides. Score 0.411 Round 3: 191 peptides, 31 chains. Longest chain 12 peptides. Score 0.444 Round 4: 205 peptides, 27 chains. Longest chain 16 peptides. Score 0.550 Round 5: 205 peptides, 28 chains. Longest chain 26 peptides. Score 0.536 Taking the results from Round 4 Chains 27, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5446 reflections ( 99.91 % complete ) and 5407 restraints for refining 2473 atoms. 4722 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3120 (Rfree = 0.000) for 2473 atoms. Found 15 (15 requested) and removed 27 (7 requested) atoms. Cycle 2: After refmac, R = 0.2623 (Rfree = 0.000) for 2423 atoms. Found 13 (15 requested) and removed 17 (7 requested) atoms. Cycle 3: After refmac, R = 0.2464 (Rfree = 0.000) for 2399 atoms. Found 10 (15 requested) and removed 17 (7 requested) atoms. Cycle 4: After refmac, R = 0.2041 (Rfree = 0.000) for 2384 atoms. Found 1 (15 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.2233 (Rfree = 0.000) for 2368 atoms. Found 6 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 2.91 Search for helices and strands: 0 residues in 0 chains, 2438 seeds are put forward Round 1: 192 peptides, 33 chains. Longest chain 14 peptides. Score 0.416 Round 2: 219 peptides, 30 chains. Longest chain 21 peptides. Score 0.551 Round 3: 218 peptides, 28 chains. Longest chain 23 peptides. Score 0.575 Round 4: 218 peptides, 29 chains. Longest chain 16 peptides. Score 0.562 Round 5: 228 peptides, 30 chains. Longest chain 21 peptides. Score 0.578 Taking the results from Round 5 Chains 31, Residues 198, Estimated correctness of the model 5.9 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5446 reflections ( 99.91 % complete ) and 5326 restraints for refining 2471 atoms. 4527 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2822 (Rfree = 0.000) for 2471 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 7: After refmac, R = 0.2602 (Rfree = 0.000) for 2437 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 8: After refmac, R = 0.2423 (Rfree = 0.000) for 2429 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 9: After refmac, R = 0.2044 (Rfree = 0.000) for 2427 atoms. Found 10 (15 requested) and removed 9 (7 requested) atoms. Cycle 10: After refmac, R = 0.2071 (Rfree = 0.000) for 2423 atoms. Found 10 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 2.95 Search for helices and strands: 0 residues in 0 chains, 2496 seeds are put forward Round 1: 174 peptides, 31 chains. Longest chain 12 peptides. Score 0.380 Round 2: 188 peptides, 26 chains. Longest chain 29 peptides. Score 0.509 Round 3: 203 peptides, 28 chains. Longest chain 16 peptides. Score 0.529 Round 4: 214 peptides, 34 chains. Longest chain 18 peptides. Score 0.478 Round 5: 216 peptides, 30 chains. Longest chain 19 peptides. Score 0.542 Taking the results from Round 5 Chains 30, Residues 186, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5446 reflections ( 99.91 % complete ) and 5512 restraints for refining 2473 atoms. 4798 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2793 (Rfree = 0.000) for 2473 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 12: After refmac, R = 0.2792 (Rfree = 0.000) for 2446 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 13: After refmac, R = 0.2761 (Rfree = 0.000) for 2423 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 14: After refmac, R = 0.2743 (Rfree = 0.000) for 2409 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 15: After refmac, R = 0.2795 (Rfree = 0.000) for 2401 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 2.96 Search for helices and strands: 0 residues in 0 chains, 2479 seeds are put forward Round 1: 186 peptides, 33 chains. Longest chain 14 peptides. Score 0.393 Round 2: 189 peptides, 30 chains. Longest chain 17 peptides. Score 0.452 Round 3: 203 peptides, 34 chains. Longest chain 17 peptides. Score 0.440 Round 4: 213 peptides, 34 chains. Longest chain 17 peptides. Score 0.475 Round 5: 220 peptides, 33 chains. Longest chain 17 peptides. Score 0.513 Taking the results from Round 5 Chains 33, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5446 reflections ( 99.91 % complete ) and 5441 restraints for refining 2472 atoms. 4726 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2895 (Rfree = 0.000) for 2472 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 17: After refmac, R = 0.2734 (Rfree = 0.000) for 2446 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 18: After refmac, R = 0.2756 (Rfree = 0.000) for 2432 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 19: After refmac, R = 0.2689 (Rfree = 0.000) for 2426 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 20: After refmac, R = 0.2600 (Rfree = 0.000) for 2418 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.01 Search for helices and strands: 0 residues in 0 chains, 2500 seeds are put forward Round 1: 167 peptides, 31 chains. Longest chain 12 peptides. Score 0.353 Round 2: 189 peptides, 30 chains. Longest chain 16 peptides. Score 0.452 Round 3: 187 peptides, 29 chains. Longest chain 14 peptides. Score 0.460 Round 4: 199 peptides, 32 chains. Longest chain 13 peptides. Score 0.457 Round 5: 204 peptides, 33 chains. Longest chain 20 peptides. Score 0.459 Taking the results from Round 3 Chains 29, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5446 reflections ( 99.91 % complete ) and 5617 restraints for refining 2473 atoms. 5014 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3030 (Rfree = 0.000) for 2473 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 22: After refmac, R = 0.2866 (Rfree = 0.000) for 2449 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 23: After refmac, R = 0.2862 (Rfree = 0.000) for 2436 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 24: After refmac, R = 0.2933 (Rfree = 0.000) for 2430 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 25: After refmac, R = 0.2815 (Rfree = 0.000) for 2424 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 2.98 Search for helices and strands: 0 residues in 0 chains, 2485 seeds are put forward Round 1: 144 peptides, 22 chains. Longest chain 15 peptides. Score 0.416 Round 2: 172 peptides, 27 chains. Longest chain 16 peptides. Score 0.438 Round 3: 172 peptides, 24 chains. Longest chain 23 peptides. Score 0.485 Round 4: 178 peptides, 27 chains. Longest chain 21 peptides. Score 0.460 Round 5: 176 peptides, 26 chains. Longest chain 22 peptides. Score 0.468 Taking the results from Round 3 Chains 24, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5446 reflections ( 99.91 % complete ) and 5626 restraints for refining 2472 atoms. 5058 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3020 (Rfree = 0.000) for 2472 atoms. Found 15 (15 requested) and removed 25 (7 requested) atoms. Cycle 27: After refmac, R = 0.2905 (Rfree = 0.000) for 2449 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 28: After refmac, R = 0.2906 (Rfree = 0.000) for 2439 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 29: After refmac, R = 0.2834 (Rfree = 0.000) for 2429 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 30: After refmac, R = 0.2314 (Rfree = 0.000) for 2419 atoms. Found 13 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 2.97 Search for helices and strands: 0 residues in 0 chains, 2476 seeds are put forward Round 1: 151 peptides, 26 chains. Longest chain 12 peptides. Score 0.375 Round 2: 169 peptides, 26 chains. Longest chain 16 peptides. Score 0.443 Round 3: 170 peptides, 25 chains. Longest chain 16 peptides. Score 0.463 Round 4: 165 peptides, 23 chains. Longest chain 16 peptides. Score 0.477 Round 5: 167 peptides, 24 chains. Longest chain 16 peptides. Score 0.468 Taking the results from Round 4 Chains 23, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5446 reflections ( 99.91 % complete ) and 5579 restraints for refining 2473 atoms. 5034 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2913 (Rfree = 0.000) for 2473 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 32: After refmac, R = 0.2903 (Rfree = 0.000) for 2446 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 33: After refmac, R = 0.2852 (Rfree = 0.000) for 2442 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 34: After refmac, R = 0.2439 (Rfree = 0.000) for 2434 atoms. Found 9 (15 requested) and removed 11 (7 requested) atoms. Cycle 35: After refmac, R = 0.2796 (Rfree = 0.000) for 2429 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 2.97 Search for helices and strands: 0 residues in 0 chains, 2495 seeds are put forward Round 1: 137 peptides, 27 chains. Longest chain 10 peptides. Score 0.299 Round 2: 167 peptides, 27 chains. Longest chain 11 peptides. Score 0.419 Round 3: 164 peptides, 24 chains. Longest chain 15 peptides. Score 0.457 Round 4: 162 peptides, 24 chains. Longest chain 13 peptides. Score 0.450 Round 5: 165 peptides, 22 chains. Longest chain 16 peptides. Score 0.492 Taking the results from Round 5 Chains 22, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5446 reflections ( 99.91 % complete ) and 5557 restraints for refining 2472 atoms. 5007 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3064 (Rfree = 0.000) for 2472 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 37: After refmac, R = 0.2825 (Rfree = 0.000) for 2455 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 38: After refmac, R = 0.2874 (Rfree = 0.000) for 2445 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 39: After refmac, R = 0.2819 (Rfree = 0.000) for 2436 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 40: After refmac, R = 0.2900 (Rfree = 0.000) for 2434 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 2.97 Search for helices and strands: 0 residues in 0 chains, 2488 seeds are put forward Round 1: 136 peptides, 26 chains. Longest chain 14 peptides. Score 0.313 Round 2: 131 peptides, 23 chains. Longest chain 13 peptides. Score 0.347 Round 3: 140 peptides, 23 chains. Longest chain 14 peptides. Score 0.383 Round 4: 149 peptides, 25 chains. Longest chain 14 peptides. Score 0.384 Round 5: 146 peptides, 23 chains. Longest chain 12 peptides. Score 0.407 Taking the results from Round 5 Chains 23, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5446 reflections ( 99.91 % complete ) and 5732 restraints for refining 2473 atoms. 5263 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3039 (Rfree = 0.000) for 2473 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 42: After refmac, R = 0.3089 (Rfree = 0.000) for 2460 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 43: After refmac, R = 0.2972 (Rfree = 0.000) for 2442 atoms. Found 15 (15 requested) and removed 25 (7 requested) atoms. Cycle 44: After refmac, R = 0.2993 (Rfree = 0.000) for 2423 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 45: After refmac, R = 0.2897 (Rfree = 0.000) for 2415 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 2.98 Search for helices and strands: 0 residues in 0 chains, 2483 seeds are put forward Round 1: 126 peptides, 23 chains. Longest chain 11 peptides. Score 0.326 Round 2: 151 peptides, 26 chains. Longest chain 13 peptides. Score 0.375 Round 3: 147 peptides, 26 chains. Longest chain 11 peptides. Score 0.359 Round 4: 147 peptides, 26 chains. Longest chain 14 peptides. Score 0.359 Round 5: 155 peptides, 25 chains. Longest chain 11 peptides. Score 0.407 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 130, 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 1vjz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5446 reflections ( 99.91 % complete ) and 5569 restraints for refining 2473 atoms. 5074 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2921 (Rfree = 0.000) for 2473 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2942 (Rfree = 0.000) for 2449 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2916 (Rfree = 0.000) for 2437 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2784 (Rfree = 0.000) for 2422 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:11:11 GMT 2018 Job finished. TimeTaking 48.01 Used memory is bytes: 4496248