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 2a2m-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a2m-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a2m-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-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/2a2m-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-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 22:23:08 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/2a2m-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-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 577 and 0 Target number of residues in the AU: 577 Target solvent content: 0.6704 Checking the provided sequence file Detected sequence length: 258 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 516 Adjusted target solvent content: 0.71 Input MTZ file: 2a2m-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: 209 Cell parameters: 283.292 283.292 283.292 90.000 90.000 90.000 Input sequence file: 2a2m-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 4128 target number of atoms Had to go as low as 1.00 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: 163.559 4.002 Wilson plot Bfac: 92.41 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 8673 reflections ( 99.66 % complete ) and 0 restraints for refining 4580 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3496 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3497 (Rfree = 0.000) for 4580 atoms. Found 21 (21 requested) and removed 52 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.85 2.86 Search for helices and strands: 0 residues in 0 chains, 4705 seeds are put forward NCS extension: 0 residues added, 4705 seeds are put forward Round 1: 257 peptides, 37 chains. Longest chain 17 peptides. Score 0.399 Round 2: 288 peptides, 30 chains. Longest chain 21 peptides. Score 0.506 Round 3: 292 peptides, 24 chains. Longest chain 24 peptides. Score 0.557 Round 4: 289 peptides, 27 chains. Longest chain 20 peptides. Score 0.530 Round 5: 282 peptides, 25 chains. Longest chain 38 peptides. Score 0.535 Taking the results from Round 3 Chains 30, Residues 268, Estimated correctness of the model 0.0 % 4 chains (45 residues) have been docked in sequence ------------------------------------------------------ 8673 reflections ( 99.66 % complete ) and 7952 restraints for refining 3727 atoms. 6744 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2831 (Rfree = 0.000) for 3727 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 2: After refmac, R = 0.2775 (Rfree = 0.000) for 3627 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 3: After refmac, R = 0.2733 (Rfree = 0.000) for 3573 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 4: After refmac, R = 0.2641 (Rfree = 0.000) for 3526 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 5: After refmac, R = 0.2404 (Rfree = 0.000) for 3494 atoms. Found 7 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 2.78 Search for helices and strands: 0 residues in 0 chains, 3653 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3670 seeds are put forward Round 1: 285 peptides, 29 chains. Longest chain 23 peptides. Score 0.509 Round 2: 295 peptides, 28 chains. Longest chain 24 peptides. Score 0.532 Round 3: 282 peptides, 25 chains. Longest chain 29 peptides. Score 0.535 Round 4: 283 peptides, 24 chains. Longest chain 39 peptides. Score 0.544 Round 5: 286 peptides, 27 chains. Longest chain 23 peptides. Score 0.526 Taking the results from Round 4 Chains 28, Residues 259, Estimated correctness of the model 0.0 % 3 chains (52 residues) have been docked in sequence ------------------------------------------------------ 8673 reflections ( 99.66 % complete ) and 7583 restraints for refining 3728 atoms. 6319 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2688 (Rfree = 0.000) for 3728 atoms. Found 17 (17 requested) and removed 32 (8 requested) atoms. Cycle 7: After refmac, R = 0.2754 (Rfree = 0.000) for 3650 atoms. Found 17 (17 requested) and removed 39 (8 requested) atoms. Cycle 8: After refmac, R = 0.2602 (Rfree = 0.000) for 3591 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 9: After refmac, R = 0.2601 (Rfree = 0.000) for 3546 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 10: After refmac, R = 0.2337 (Rfree = 0.000) for 3499 atoms. Found 8 (16 requested) and removed 20 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.76 2.79 Search for helices and strands: 0 residues in 0 chains, 3705 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3733 seeds are put forward Round 1: 282 peptides, 30 chains. Longest chain 23 peptides. Score 0.497 Round 2: 285 peptides, 28 chains. Longest chain 28 peptides. Score 0.517 Round 3: 296 peptides, 30 chains. Longest chain 25 peptides. Score 0.519 Round 4: 284 peptides, 26 chains. Longest chain 25 peptides. Score 0.530 Round 5: 288 peptides, 23 chains. Longest chain 37 peptides. Score 0.559 Taking the results from Round 5 Chains 25, Residues 265, Estimated correctness of the model 0.0 % 2 chains (48 residues) have been docked in sequence ------------------------------------------------------ 8673 reflections ( 99.66 % complete ) and 7625 restraints for refining 3728 atoms. 6400 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2637 (Rfree = 0.000) for 3728 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 12: After refmac, R = 0.2622 (Rfree = 0.000) for 3665 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 13: After refmac, R = 0.2637 (Rfree = 0.000) for 3614 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 14: After refmac, R = 0.2379 (Rfree = 0.000) for 3572 atoms. Found 12 (17 requested) and removed 17 (8 requested) atoms. Cycle 15: After refmac, R = 0.2339 (Rfree = 0.000) for 3541 atoms. Found 7 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 2.80 Search for helices and strands: 0 residues in 0 chains, 3703 seeds are put forward NCS extension: 39 residues added (1 deleted due to clashes), 3742 seeds are put forward Round 1: 259 peptides, 31 chains. Longest chain 19 peptides. Score 0.452 Round 2: 269 peptides, 24 chains. Longest chain 46 peptides. Score 0.523 Round 3: 281 peptides, 29 chains. Longest chain 29 peptides. Score 0.503 Round 4: 274 peptides, 22 chains. Longest chain 44 peptides. Score 0.546 Round 5: 281 peptides, 25 chains. Longest chain 30 peptides. Score 0.533 Taking the results from Round 4 Chains 25, Residues 252, Estimated correctness of the model 0.0 % 3 chains (62 residues) have been docked in sequence ------------------------------------------------------ 8673 reflections ( 99.66 % complete ) and 7491 restraints for refining 3728 atoms. 6241 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2729 (Rfree = 0.000) for 3728 atoms. Found 17 (17 requested) and removed 41 (8 requested) atoms. Cycle 17: After refmac, R = 0.2620 (Rfree = 0.000) for 3650 atoms. Found 17 (17 requested) and removed 37 (8 requested) atoms. Cycle 18: After refmac, R = 0.2621 (Rfree = 0.000) for 3593 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 19: After refmac, R = 0.2638 (Rfree = 0.000) for 3550 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 20: After refmac, R = 0.2417 (Rfree = 0.000) for 3511 atoms. Found 9 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.82 2.84 Search for helices and strands: 0 residues in 0 chains, 3712 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 3742 seeds are put forward Round 1: 258 peptides, 28 chains. Longest chain 28 peptides. Score 0.474 Round 2: 286 peptides, 23 chains. Longest chain 32 peptides. Score 0.556 Round 3: 270 peptides, 25 chains. Longest chain 28 peptides. Score 0.517 Round 4: 271 peptides, 28 chains. Longest chain 26 peptides. Score 0.495 Round 5: 277 peptides, 27 chains. Longest chain 20 peptides. Score 0.512 Taking the results from Round 2 Chains 28, Residues 263, Estimated correctness of the model 0.0 % 4 chains (71 residues) have been docked in sequence ------------------------------------------------------ 8673 reflections ( 99.66 % complete ) and 6962 restraints for refining 3728 atoms. 5556 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2530 (Rfree = 0.000) for 3728 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 22: After refmac, R = 0.2480 (Rfree = 0.000) for 3669 atoms. Found 17 (17 requested) and removed 32 (8 requested) atoms. Cycle 23: After refmac, R = 0.2342 (Rfree = 0.000) for 3637 atoms. Found 12 (17 requested) and removed 25 (8 requested) atoms. Cycle 24: After refmac, R = 0.2350 (Rfree = 0.000) for 3610 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 25: After refmac, R = 0.2263 (Rfree = 0.000) for 3596 atoms. Found 13 (17 requested) and removed 20 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.77 2.80 Search for helices and strands: 0 residues in 0 chains, 3779 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 3805 seeds are put forward Round 1: 252 peptides, 31 chains. Longest chain 20 peptides. Score 0.440 Round 2: 277 peptides, 26 chains. Longest chain 37 peptides. Score 0.520 Round 3: 261 peptides, 26 chains. Longest chain 32 peptides. Score 0.495 Round 4: 279 peptides, 26 chains. Longest chain 42 peptides. Score 0.523 Round 5: 269 peptides, 24 chains. Longest chain 29 peptides. Score 0.523 Taking the results from Round 5 Chains 25, Residues 245, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8673 reflections ( 99.66 % complete ) and 8342 restraints for refining 3727 atoms. 7357 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2653 (Rfree = 0.000) for 3727 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 27: After refmac, R = 0.2554 (Rfree = 0.000) for 3683 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 28: After refmac, R = 0.2483 (Rfree = 0.000) for 3652 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 29: After refmac, R = 0.2435 (Rfree = 0.000) for 3624 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 30: After refmac, R = 0.2431 (Rfree = 0.000) for 3602 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.82 2.84 Search for helices and strands: 0 residues in 0 chains, 3838 seeds are put forward NCS extension: 36 residues added (4 deleted due to clashes), 3874 seeds are put forward Round 1: 266 peptides, 37 chains. Longest chain 19 peptides. Score 0.415 Round 2: 271 peptides, 30 chains. Longest chain 21 peptides. Score 0.480 Round 3: 284 peptides, 28 chains. Longest chain 25 peptides. Score 0.515 Round 4: 279 peptides, 29 chains. Longest chain 25 peptides. Score 0.500 Round 5: 255 peptides, 29 chains. Longest chain 18 peptides. Score 0.461 Taking the results from Round 3 Chains 32, Residues 256, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 8673 reflections ( 99.66 % complete ) and 8087 restraints for refining 3727 atoms. 7030 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2678 (Rfree = 0.000) for 3727 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 32: After refmac, R = 0.2544 (Rfree = 0.000) for 3654 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 33: After refmac, R = 0.2546 (Rfree = 0.000) for 3616 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 34: After refmac, R = 0.2443 (Rfree = 0.000) for 3589 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 35: After refmac, R = 0.2474 (Rfree = 0.000) for 3567 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.77 2.80 Search for helices and strands: 0 residues in 0 chains, 3767 seeds are put forward NCS extension: 0 residues added, 3767 seeds are put forward Round 1: 260 peptides, 38 chains. Longest chain 18 peptides. Score 0.396 Round 2: 296 peptides, 35 chains. Longest chain 20 peptides. Score 0.481 Round 3: 266 peptides, 31 chains. Longest chain 21 peptides. Score 0.463 Round 4: 277 peptides, 30 chains. Longest chain 24 peptides. Score 0.489 Round 5: 274 peptides, 30 chains. Longest chain 22 peptides. Score 0.484 Taking the results from Round 4 Chains 30, Residues 247, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8673 reflections ( 99.66 % complete ) and 8356 restraints for refining 3728 atoms. 7398 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2521 (Rfree = 0.000) for 3728 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 37: After refmac, R = 0.2462 (Rfree = 0.000) for 3684 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 38: After refmac, R = 0.2448 (Rfree = 0.000) for 3650 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 39: After refmac, R = 0.2398 (Rfree = 0.000) for 3630 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 40: After refmac, R = 0.2406 (Rfree = 0.000) for 3609 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.77 2.80 Search for helices and strands: 0 residues in 0 chains, 3860 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 3897 seeds are put forward Round 1: 242 peptides, 33 chains. Longest chain 17 peptides. Score 0.406 Round 2: 263 peptides, 29 chains. Longest chain 21 peptides. Score 0.474 Round 3: 268 peptides, 23 chains. Longest chain 31 peptides. Score 0.529 Round 4: 262 peptides, 26 chains. Longest chain 21 peptides. Score 0.497 Round 5: 266 peptides, 25 chains. Longest chain 23 peptides. Score 0.511 Taking the results from Round 3 Chains 25, Residues 245, Estimated correctness of the model 0.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 8673 reflections ( 99.66 % complete ) and 7837 restraints for refining 3728 atoms. 6741 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2630 (Rfree = 0.000) for 3728 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 42: After refmac, R = 0.2509 (Rfree = 0.000) for 3685 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 43: After refmac, R = 0.2518 (Rfree = 0.000) for 3656 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 44: After refmac, R = 0.2495 (Rfree = 0.000) for 3629 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 45: After refmac, R = 0.2504 (Rfree = 0.000) for 3601 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.76 2.79 Search for helices and strands: 0 residues in 0 chains, 3787 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3815 seeds are put forward Round 1: 241 peptides, 36 chains. Longest chain 13 peptides. Score 0.378 Round 2: 245 peptides, 28 chains. Longest chain 21 peptides. Score 0.453 Round 3: 251 peptides, 26 chains. Longest chain 20 peptides. Score 0.479 Round 4: 254 peptides, 27 chains. Longest chain 29 peptides. Score 0.476 Round 5: 259 peptides, 27 chains. Longest chain 31 peptides. Score 0.484 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 232, Estimated correctness of the model 0.0 % 2 chains (39 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 2a2m-4_warpNtrace.pdb as input Building loops using Loopy2018 28 chains (232 residues) following loop building 2 chains (39 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8673 reflections ( 99.66 % complete ) and 7771 restraints for refining 3728 atoms. 6672 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2697 (Rfree = 0.000) for 3728 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2560 (Rfree = 0.000) for 3673 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2623 (Rfree = 0.000) for 3630 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2591 (Rfree = 0.000) for 3586 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 224.95