Sun 23 Dec 22:22:59 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 1vl0-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl0-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl0-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-4.0-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/1vl0-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-4.0-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 22:23:09 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/1vl0-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-4.0-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 671 and 0 Target number of residues in the AU: 671 Target solvent content: 0.6548 Checking the provided sequence file Detected sequence length: 292 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 876 Adjusted target solvent content: 0.55 Input MTZ file: 1vl0-4.0-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: 20 Cell parameters: 106.471 130.661 151.225 90.000 90.000 90.000 Input sequence file: 1vl0-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 7008 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: 29.987 4.000 Wilson plot Bfac: 81.21 9090 reflections ( 98.72 % complete ) and 0 restraints for refining 7724 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3855 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3449 (Rfree = 0.000) for 7724 atoms. Found 36 (36 requested) and removed 193 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.40 Search for helices and strands: 0 residues in 0 chains, 7598 seeds are put forward NCS extension: 0 residues added, 7598 seeds are put forward Round 1: 167 peptides, 40 chains. Longest chain 6 peptides. Score 0.183 Round 2: 238 peptides, 52 chains. Longest chain 8 peptides. Score 0.229 Round 3: 267 peptides, 56 chains. Longest chain 9 peptides. Score 0.252 Round 4: 273 peptides, 55 chains. Longest chain 10 peptides. Score 0.271 Round 5: 277 peptides, 55 chains. Longest chain 10 peptides. Score 0.278 Taking the results from Round 5 Chains 55, Residues 222, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 15110 restraints for refining 6326 atoms. 14238 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2796 (Rfree = 0.000) for 6326 atoms. Found 20 (30 requested) and removed 70 (15 requested) atoms. Cycle 2: After refmac, R = 0.3046 (Rfree = 0.000) for 6218 atoms. Found 19 (29 requested) and removed 46 (14 requested) atoms. Cycle 3: After refmac, R = 0.2558 (Rfree = 0.000) for 6130 atoms. Found 13 (29 requested) and removed 27 (14 requested) atoms. Cycle 4: After refmac, R = 0.2892 (Rfree = 0.000) for 6084 atoms. Found 18 (29 requested) and removed 34 (14 requested) atoms. Cycle 5: After refmac, R = 0.2843 (Rfree = 0.000) for 6036 atoms. Found 22 (28 requested) and removed 41 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.36 Search for helices and strands: 0 residues in 0 chains, 6107 seeds are put forward NCS extension: 0 residues added, 6107 seeds are put forward Round 1: 218 peptides, 49 chains. Longest chain 8 peptides. Score 0.213 Round 2: 330 peptides, 66 chains. Longest chain 11 peptides. Score 0.289 Round 3: 330 peptides, 65 chains. Longest chain 9 peptides. Score 0.297 Round 4: 344 peptides, 70 chains. Longest chain 11 peptides. Score 0.284 Round 5: 356 peptides, 70 chains. Longest chain 10 peptides. Score 0.305 Taking the results from Round 5 Chains 70, Residues 286, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 12879 restraints for refining 5728 atoms. 11769 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2819 (Rfree = 0.000) for 5728 atoms. Found 27 (27 requested) and removed 52 (13 requested) atoms. Cycle 7: After refmac, R = 0.2655 (Rfree = 0.000) for 5636 atoms. Found 27 (27 requested) and removed 39 (13 requested) atoms. Cycle 8: After refmac, R = 0.2525 (Rfree = 0.000) for 5580 atoms. Found 26 (26 requested) and removed 35 (13 requested) atoms. Cycle 9: After refmac, R = 0.2447 (Rfree = 0.000) for 5538 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. Cycle 10: After refmac, R = 0.1991 (Rfree = 0.000) for 5514 atoms. Found 12 (26 requested) and removed 26 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 3.39 Search for helices and strands: 0 residues in 0 chains, 5617 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 5620 seeds are put forward Round 1: 292 peptides, 60 chains. Longest chain 10 peptides. Score 0.267 Round 2: 337 peptides, 62 chains. Longest chain 11 peptides. Score 0.331 Round 3: 343 peptides, 62 chains. Longest chain 20 peptides. Score 0.341 Round 4: 352 peptides, 61 chains. Longest chain 16 peptides. Score 0.363 Round 5: 357 peptides, 59 chains. Longest chain 16 peptides. Score 0.385 Taking the results from Round 5 Chains 59, Residues 298, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 12642 restraints for refining 5760 atoms. 11470 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2662 (Rfree = 0.000) for 5760 atoms. Found 27 (27 requested) and removed 52 (13 requested) atoms. Cycle 12: After refmac, R = 0.2491 (Rfree = 0.000) for 5674 atoms. Found 27 (27 requested) and removed 34 (13 requested) atoms. Cycle 13: After refmac, R = 0.2394 (Rfree = 0.000) for 5616 atoms. Found 26 (26 requested) and removed 35 (13 requested) atoms. Cycle 14: After refmac, R = 0.2374 (Rfree = 0.000) for 5575 atoms. Found 26 (26 requested) and removed 31 (13 requested) atoms. Cycle 15: After refmac, R = 0.2351 (Rfree = 0.000) for 5539 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.44 Search for helices and strands: 0 residues in 0 chains, 5649 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 5671 seeds are put forward Round 1: 273 peptides, 58 chains. Longest chain 8 peptides. Score 0.247 Round 2: 335 peptides, 60 chains. Longest chain 14 peptides. Score 0.342 Round 3: 331 peptides, 61 chains. Longest chain 11 peptides. Score 0.328 Round 4: 345 peptides, 57 chains. Longest chain 14 peptides. Score 0.380 Round 5: 355 peptides, 61 chains. Longest chain 12 peptides. Score 0.368 Taking the results from Round 4 Chains 58, Residues 288, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 12557 restraints for refining 5738 atoms. 11431 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2665 (Rfree = 0.000) for 5738 atoms. Found 27 (27 requested) and removed 44 (13 requested) atoms. Cycle 17: After refmac, R = 0.2485 (Rfree = 0.000) for 5678 atoms. Found 27 (27 requested) and removed 43 (13 requested) atoms. Cycle 18: After refmac, R = 0.2033 (Rfree = 0.000) for 5626 atoms. Found 14 (26 requested) and removed 23 (13 requested) atoms. Cycle 19: After refmac, R = 0.1951 (Rfree = 0.000) for 5596 atoms. Found 10 (26 requested) and removed 20 (13 requested) atoms. Cycle 20: After refmac, R = 0.2027 (Rfree = 0.000) for 5570 atoms. Found 8 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 3.40 Search for helices and strands: 0 residues in 0 chains, 5668 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5687 seeds are put forward Round 1: 325 peptides, 70 chains. Longest chain 8 peptides. Score 0.251 Round 2: 372 peptides, 65 chains. Longest chain 14 peptides. Score 0.367 Round 3: 376 peptides, 68 chains. Longest chain 14 peptides. Score 0.352 Round 4: 390 peptides, 67 chains. Longest chain 17 peptides. Score 0.382 Round 5: 372 peptides, 63 chains. Longest chain 13 peptides. Score 0.381 Taking the results from Round 4 Chains 67, Residues 323, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 13062 restraints for refining 5979 atoms. 11837 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2587 (Rfree = 0.000) for 5979 atoms. Found 28 (28 requested) and removed 64 (14 requested) atoms. Cycle 22: After refmac, R = 0.2479 (Rfree = 0.000) for 5893 atoms. Found 28 (28 requested) and removed 50 (14 requested) atoms. Cycle 23: After refmac, R = 0.2487 (Rfree = 0.000) for 5832 atoms. Found 27 (27 requested) and removed 41 (13 requested) atoms. Cycle 24: After refmac, R = 0.2387 (Rfree = 0.000) for 5784 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 25: After refmac, R = 0.2433 (Rfree = 0.000) for 5760 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.37 Search for helices and strands: 0 residues in 0 chains, 5878 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 5902 seeds are put forward Round 1: 296 peptides, 63 chains. Longest chain 9 peptides. Score 0.251 Round 2: 337 peptides, 63 chains. Longest chain 11 peptides. Score 0.323 Round 3: 369 peptides, 67 chains. Longest chain 13 peptides. Score 0.348 Round 4: 373 peptides, 65 chains. Longest chain 11 peptides. Score 0.369 Round 5: 383 peptides, 63 chains. Longest chain 13 peptides. Score 0.398 Taking the results from Round 5 Chains 63, Residues 320, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 13225 restraints for refining 6019 atoms. 11985 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2452 (Rfree = 0.000) for 6019 atoms. Found 28 (28 requested) and removed 48 (14 requested) atoms. Cycle 27: After refmac, R = 0.2403 (Rfree = 0.000) for 5934 atoms. Found 28 (28 requested) and removed 43 (14 requested) atoms. Cycle 28: After refmac, R = 0.2390 (Rfree = 0.000) for 5878 atoms. Found 28 (28 requested) and removed 30 (14 requested) atoms. Cycle 29: After refmac, R = 0.2428 (Rfree = 0.000) for 5843 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 30: After refmac, R = 0.2389 (Rfree = 0.000) for 5812 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.39 Search for helices and strands: 0 residues in 0 chains, 5944 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 5965 seeds are put forward Round 1: 289 peptides, 62 chains. Longest chain 9 peptides. Score 0.246 Round 2: 327 peptides, 60 chains. Longest chain 12 peptides. Score 0.328 Round 3: 325 peptides, 56 chains. Longest chain 16 peptides. Score 0.354 Round 4: 321 peptides, 55 chains. Longest chain 12 peptides. Score 0.355 Round 5: 327 peptides, 55 chains. Longest chain 14 peptides. Score 0.365 Taking the results from Round 5 Chains 55, Residues 272, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 13130 restraints for refining 5886 atoms. 12087 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2488 (Rfree = 0.000) for 5886 atoms. Found 27 (27 requested) and removed 39 (13 requested) atoms. Cycle 32: After refmac, R = 0.2478 (Rfree = 0.000) for 5820 atoms. Found 27 (27 requested) and removed 45 (13 requested) atoms. Cycle 33: After refmac, R = 0.2350 (Rfree = 0.000) for 5772 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 34: After refmac, R = 0.2444 (Rfree = 0.000) for 5747 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 35: After refmac, R = 0.2312 (Rfree = 0.000) for 5725 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.36 Search for helices and strands: 0 residues in 0 chains, 5842 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5856 seeds are put forward Round 1: 229 peptides, 52 chains. Longest chain 8 peptides. Score 0.211 Round 2: 290 peptides, 55 chains. Longest chain 12 peptides. Score 0.302 Round 3: 279 peptides, 48 chains. Longest chain 13 peptides. Score 0.336 Round 4: 299 peptides, 53 chains. Longest chain 15 peptides. Score 0.333 Round 5: 305 peptides, 55 chains. Longest chain 16 peptides. Score 0.328 Taking the results from Round 3 Chains 48, Residues 231, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 12324 restraints for refining 5676 atoms. 11448 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2494 (Rfree = 0.000) for 5676 atoms. Found 26 (26 requested) and removed 46 (13 requested) atoms. Cycle 37: After refmac, R = 0.2543 (Rfree = 0.000) for 5633 atoms. Found 26 (26 requested) and removed 51 (13 requested) atoms. Cycle 38: After refmac, R = 0.2435 (Rfree = 0.000) for 5583 atoms. Found 26 (26 requested) and removed 38 (13 requested) atoms. Cycle 39: After refmac, R = 0.2478 (Rfree = 0.000) for 5566 atoms. Found 26 (26 requested) and removed 30 (13 requested) atoms. Cycle 40: After refmac, R = 0.2031 (Rfree = 0.000) for 5547 atoms. Found 12 (26 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.38 Search for helices and strands: 0 residues in 0 chains, 5624 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 5644 seeds are put forward Round 1: 260 peptides, 59 chains. Longest chain 8 peptides. Score 0.215 Round 2: 270 peptides, 49 chains. Longest chain 9 peptides. Score 0.312 Round 3: 287 peptides, 54 chains. Longest chain 11 peptides. Score 0.304 Round 4: 300 peptides, 57 chains. Longest chain 14 peptides. Score 0.304 Round 5: 278 peptides, 48 chains. Longest chain 10 peptides. Score 0.334 Taking the results from Round 5 Chains 48, Residues 230, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9090 reflections ( 98.72 % complete ) and 12993 restraints for refining 5870 atoms. 12121 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2631 (Rfree = 0.000) for 5870 atoms. Found 27 (27 requested) and removed 52 (13 requested) atoms. Cycle 42: After refmac, R = 0.2631 (Rfree = 0.000) for 5809 atoms. Found 27 (27 requested) and removed 38 (13 requested) atoms. Cycle 43: After refmac, R = 0.2458 (Rfree = 0.000) for 5770 atoms. Found 27 (27 requested) and removed 34 (13 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2286 (Rfree = 0.000) for 5734 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. Cycle 45: After refmac, R = 0.2329 (Rfree = 0.000) for 5707 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 3.40 Search for helices and strands: 0 residues in 0 chains, 5793 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5805 seeds are put forward Round 1: 222 peptides, 50 chains. Longest chain 8 peptides. Score 0.213 Round 2: 243 peptides, 48 chains. Longest chain 17 peptides. Score 0.271 Round 3: 238 peptides, 45 chains. Longest chain 18 peptides. Score 0.286 Round 4: 241 peptides, 46 chains. Longest chain 18 peptides. Score 0.283 Round 5: 243 peptides, 45 chains. Longest chain 18 peptides. Score 0.295 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 198, 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 1vl0-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9090 reflections ( 98.72 % complete ) and 12947 restraints for refining 5746 atoms. 12200 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2518 (Rfree = 0.000) for 5746 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2538 (Rfree = 0.000) for 5710 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2454 (Rfree = 0.000) for 5679 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1932 (Rfree = 0.000) for 5641 atoms. TimeTaking 76.25