Mon 24 Dec 00:43:35 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fno-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fno-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fno-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-3.6-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:43:40 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-3.6-parrot-mrncs/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 392 and 0 Target number of residues in the AU: 392 Target solvent content: 0.6387 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 496 Adjusted target solvent content: 0.54 Input MTZ file: 2fno-3.6-parrot-mrncs.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: 110.204 50.261 117.660 90.000 115.716 90.000 Input sequence file: 2fno-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3968 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 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: 106.006 3.600 Wilson plot Bfac: 71.28 6884 reflections ( 99.21 % complete ) and 0 restraints for refining 4394 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3263 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3523 (Rfree = 0.000) for 4394 atoms. Found 28 (28 requested) and removed 64 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 4468 seeds are put forward NCS extension: 0 residues added, 4468 seeds are put forward Round 1: 166 peptides, 35 chains. Longest chain 7 peptides. Score 0.256 Round 2: 226 peptides, 42 chains. Longest chain 12 peptides. Score 0.349 Round 3: 251 peptides, 41 chains. Longest chain 13 peptides. Score 0.430 Round 4: 255 peptides, 43 chains. Longest chain 12 peptides. Score 0.418 Round 5: 265 peptides, 43 chains. Longest chain 13 peptides. Score 0.444 Taking the results from Round 5 Chains 43, Residues 222, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8561 restraints for refining 3597 atoms. 7716 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2957 (Rfree = 0.000) for 3597 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. Cycle 2: After refmac, R = 0.2814 (Rfree = 0.000) for 3529 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 3: After refmac, R = 0.2629 (Rfree = 0.000) for 3488 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 4: After refmac, R = 0.2437 (Rfree = 0.000) for 3471 atoms. Found 9 (22 requested) and removed 23 (11 requested) atoms. Cycle 5: After refmac, R = 0.2351 (Rfree = 0.000) for 3451 atoms. Found 10 (22 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 3604 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3619 seeds are put forward Round 1: 242 peptides, 47 chains. Longest chain 14 peptides. Score 0.334 Round 2: 277 peptides, 46 chains. Longest chain 16 peptides. Score 0.441 Round 3: 266 peptides, 43 chains. Longest chain 16 peptides. Score 0.446 Round 4: 274 peptides, 43 chains. Longest chain 13 peptides. Score 0.467 Round 5: 276 peptides, 41 chains. Longest chain 17 peptides. Score 0.493 Taking the results from Round 5 Chains 41, Residues 235, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8117 restraints for refining 3596 atoms. 7161 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2682 (Rfree = 0.000) for 3596 atoms. Found 23 (23 requested) and removed 40 (11 requested) atoms. Cycle 7: After refmac, R = 0.2646 (Rfree = 0.000) for 3549 atoms. Found 22 (22 requested) and removed 33 (11 requested) atoms. Cycle 8: After refmac, R = 0.2351 (Rfree = 0.000) for 3524 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 9: After refmac, R = 0.2360 (Rfree = 0.000) for 3515 atoms. Found 22 (22 requested) and removed 15 (11 requested) atoms. Cycle 10: After refmac, R = 0.2330 (Rfree = 0.000) for 3516 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 3686 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3706 seeds are put forward Round 1: 259 peptides, 47 chains. Longest chain 12 peptides. Score 0.382 Round 2: 277 peptides, 41 chains. Longest chain 17 peptides. Score 0.496 Round 3: 282 peptides, 40 chains. Longest chain 18 peptides. Score 0.518 Round 4: 279 peptides, 42 chains. Longest chain 16 peptides. Score 0.490 Round 5: 275 peptides, 39 chains. Longest chain 21 peptides. Score 0.512 Taking the results from Round 3 Chains 41, Residues 242, Estimated correctness of the model 0.0 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 7788 restraints for refining 3597 atoms. 6743 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2585 (Rfree = 0.000) for 3597 atoms. Found 21 (23 requested) and removed 31 (11 requested) atoms. Cycle 12: After refmac, R = 0.2462 (Rfree = 0.000) for 3568 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. Cycle 13: After refmac, R = 0.2480 (Rfree = 0.000) for 3549 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 14: After refmac, R = 0.2470 (Rfree = 0.000) for 3530 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 15: After refmac, R = 0.2328 (Rfree = 0.000) for 3520 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 3658 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3675 seeds are put forward Round 1: 215 peptides, 38 chains. Longest chain 10 peptides. Score 0.367 Round 2: 267 peptides, 44 chains. Longest chain 13 peptides. Score 0.438 Round 3: 267 peptides, 42 chains. Longest chain 16 peptides. Score 0.460 Round 4: 253 peptides, 36 chains. Longest chain 17 peptides. Score 0.491 Round 5: 267 peptides, 40 chains. Longest chain 18 peptides. Score 0.482 Taking the results from Round 4 Chains 37, Residues 217, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8070 restraints for refining 3597 atoms. 7177 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2388 (Rfree = 0.000) for 3597 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 17: After refmac, R = 0.2228 (Rfree = 0.000) for 3575 atoms. Found 15 (23 requested) and removed 20 (11 requested) atoms. Cycle 18: After refmac, R = 0.2142 (Rfree = 0.000) for 3562 atoms. Found 9 (22 requested) and removed 17 (11 requested) atoms. Cycle 19: After refmac, R = 0.2118 (Rfree = 0.000) for 3550 atoms. Found 9 (22 requested) and removed 20 (11 requested) atoms. Cycle 20: After refmac, R = 0.2052 (Rfree = 0.000) for 3534 atoms. Found 9 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 3667 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3688 seeds are put forward Round 1: 237 peptides, 47 chains. Longest chain 10 peptides. Score 0.320 Round 2: 245 peptides, 41 chains. Longest chain 15 peptides. Score 0.414 Round 3: 255 peptides, 42 chains. Longest chain 15 peptides. Score 0.429 Round 4: 254 peptides, 40 chains. Longest chain 17 peptides. Score 0.449 Round 5: 261 peptides, 38 chains. Longest chain 15 peptides. Score 0.489 Taking the results from Round 5 Chains 40, Residues 223, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8076 restraints for refining 3596 atoms. 7179 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2468 (Rfree = 0.000) for 3596 atoms. Found 22 (23 requested) and removed 25 (11 requested) atoms. Cycle 22: After refmac, R = 0.2320 (Rfree = 0.000) for 3576 atoms. Found 15 (23 requested) and removed 19 (11 requested) atoms. Cycle 23: After refmac, R = 0.2272 (Rfree = 0.000) for 3569 atoms. Found 11 (22 requested) and removed 28 (11 requested) atoms. Cycle 24: After refmac, R = 0.2305 (Rfree = 0.000) for 3551 atoms. Found 11 (22 requested) and removed 17 (11 requested) atoms. Cycle 25: After refmac, R = 0.2207 (Rfree = 0.000) for 3542 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 3649 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3667 seeds are put forward Round 1: 244 peptides, 44 chains. Longest chain 9 peptides. Score 0.376 Round 2: 241 peptides, 39 chains. Longest chain 15 peptides. Score 0.427 Round 3: 248 peptides, 41 chains. Longest chain 15 peptides. Score 0.422 Round 4: 254 peptides, 39 chains. Longest chain 18 peptides. Score 0.460 Round 5: 233 peptides, 34 chains. Longest chain 19 peptides. Score 0.463 Taking the results from Round 5 Chains 34, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8309 restraints for refining 3597 atoms. 7547 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2390 (Rfree = 0.000) for 3597 atoms. Found 22 (23 requested) and removed 22 (11 requested) atoms. Cycle 27: After refmac, R = 0.2120 (Rfree = 0.000) for 3579 atoms. Found 4 (23 requested) and removed 18 (11 requested) atoms. Cycle 28: After refmac, R = 0.2256 (Rfree = 0.000) for 3559 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 29: After refmac, R = 0.2031 (Rfree = 0.000) for 3557 atoms. Found 11 (22 requested) and removed 14 (11 requested) atoms. Cycle 30: After refmac, R = 0.2023 (Rfree = 0.000) for 3551 atoms. Found 6 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 3695 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3720 seeds are put forward Round 1: 190 peptides, 39 chains. Longest chain 9 peptides. Score 0.279 Round 2: 221 peptides, 38 chains. Longest chain 16 peptides. Score 0.384 Round 3: 222 peptides, 37 chains. Longest chain 12 peptides. Score 0.399 Round 4: 224 peptides, 33 chains. Longest chain 12 peptides. Score 0.452 Round 5: 229 peptides, 36 chains. Longest chain 14 peptides. Score 0.430 Taking the results from Round 4 Chains 33, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8450 restraints for refining 3596 atoms. 7719 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2698 (Rfree = 0.000) for 3596 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 32: After refmac, R = 0.2189 (Rfree = 0.000) for 3581 atoms. Found 23 (23 requested) and removed 14 (11 requested) atoms. Cycle 33: After refmac, R = 0.2036 (Rfree = 0.000) for 3579 atoms. Found 11 (23 requested) and removed 13 (11 requested) atoms. Cycle 34: After refmac, R = 0.2128 (Rfree = 0.000) for 3571 atoms. Found 22 (22 requested) and removed 15 (11 requested) atoms. Cycle 35: After refmac, R = 0.2051 (Rfree = 0.000) for 3575 atoms. Found 16 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 3711 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3722 seeds are put forward Round 1: 208 peptides, 42 chains. Longest chain 9 peptides. Score 0.296 Round 2: 234 peptides, 40 chains. Longest chain 11 peptides. Score 0.396 Round 3: 229 peptides, 33 chains. Longest chain 22 peptides. Score 0.465 Round 4: 235 peptides, 36 chains. Longest chain 18 peptides. Score 0.446 Round 5: 234 peptides, 38 chains. Longest chain 16 peptides. Score 0.419 Taking the results from Round 3 Chains 33, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8340 restraints for refining 3597 atoms. 7589 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2267 (Rfree = 0.000) for 3597 atoms. Found 19 (23 requested) and removed 14 (11 requested) atoms. Cycle 37: After refmac, R = 0.2102 (Rfree = 0.000) for 3591 atoms. Found 19 (23 requested) and removed 15 (11 requested) atoms. Cycle 38: After refmac, R = 0.2080 (Rfree = 0.000) for 3585 atoms. Found 17 (23 requested) and removed 15 (11 requested) atoms. Cycle 39: After refmac, R = 0.2125 (Rfree = 0.000) for 3582 atoms. Found 22 (22 requested) and removed 12 (11 requested) atoms. Cycle 40: After refmac, R = 0.2094 (Rfree = 0.000) for 3586 atoms. Found 19 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 3722 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3748 seeds are put forward Round 1: 191 peptides, 38 chains. Longest chain 12 peptides. Score 0.295 Round 2: 213 peptides, 36 chains. Longest chain 13 peptides. Score 0.386 Round 3: 226 peptides, 39 chains. Longest chain 11 peptides. Score 0.386 Round 4: 234 peptides, 37 chains. Longest chain 13 peptides. Score 0.431 Round 5: 224 peptides, 39 chains. Longest chain 11 peptides. Score 0.380 Taking the results from Round 4 Chains 37, Residues 197, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8359 restraints for refining 3597 atoms. 7600 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2669 (Rfree = 0.000) for 3597 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Cycle 42: After refmac, R = 0.2516 (Rfree = 0.000) for 3583 atoms. Found 23 (23 requested) and removed 18 (11 requested) atoms. Cycle 43: After refmac, R = 0.2409 (Rfree = 0.000) for 3576 atoms. Found 22 (22 requested) and removed 36 (11 requested) atoms. Cycle 44: After refmac, R = 0.2480 (Rfree = 0.000) for 3552 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 45: After refmac, R = 0.2477 (Rfree = 0.000) for 3536 atoms. Found 22 (22 requested) and removed 35 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 3.34 Search for helices and strands: 0 residues in 0 chains, 3663 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3678 seeds are put forward Round 1: 133 peptides, 30 chains. Longest chain 7 peptides. Score 0.215 Round 2: 179 peptides, 34 chains. Longest chain 10 peptides. Score 0.311 Round 3: 195 peptides, 31 chains. Longest chain 16 peptides. Score 0.397 Round 4: 193 peptides, 32 chains. Longest chain 16 peptides. Score 0.379 Round 5: 194 peptides, 30 chains. Longest chain 12 peptides. Score 0.407 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 164, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2fno-3_warpNtrace.pdb as input Building loops using Loopy2018 30 chains (164 residues) following loop building 2 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6884 reflections ( 99.21 % complete ) and 8356 restraints for refining 3595 atoms. 7698 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2594 (Rfree = 0.000) for 3595 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2536 (Rfree = 0.000) for 3563 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2365 (Rfree = 0.000) for 3539 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2242 (Rfree = 0.000) for 3513 atoms. TimeTaking 41.8