Mon 24 Dec 00:00:04 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 2otm-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2otm-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2otm-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-3.4-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/2otm-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-3.4-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 00:00:09 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/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-3.4-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 388 and 0 Target number of residues in the AU: 388 Target solvent content: 0.6205 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 462 Adjusted target solvent content: 0.55 Input MTZ file: 2otm-3.4-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: 112.035 62.893 78.663 90.000 93.262 90.000 Input sequence file: 2otm-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3696 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: 78.536 3.400 Wilson plot Bfac: 61.75 7660 reflections ( 99.80 % complete ) and 0 restraints for refining 4087 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3013 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2794 (Rfree = 0.000) for 4087 atoms. Found 30 (30 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 2.99 Search for helices and strands: 0 residues in 0 chains, 4164 seeds are put forward NCS extension: 0 residues added, 4164 seeds are put forward Round 1: 266 peptides, 43 chains. Longest chain 13 peptides. Score 0.459 Round 2: 320 peptides, 35 chains. Longest chain 21 peptides. Score 0.663 Round 3: 344 peptides, 36 chains. Longest chain 25 peptides. Score 0.697 Round 4: 350 peptides, 33 chains. Longest chain 46 peptides. Score 0.730 Round 5: 345 peptides, 33 chains. Longest chain 44 peptides. Score 0.722 Taking the results from Round 4 Chains 39, Residues 317, Estimated correctness of the model 65.3 % 6 chains (84 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 A and 122 A Built loop between residues 112 B and 122 B 32 chains (321 residues) following loop building 4 chains (101 residues) in sequence following loop building ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 5991 restraints for refining 3360 atoms. 4445 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2661 (Rfree = 0.000) for 3360 atoms. Found 25 (25 requested) and removed 52 (12 requested) atoms. Cycle 2: After refmac, R = 0.2481 (Rfree = 0.000) for 3285 atoms. Found 21 (24 requested) and removed 19 (12 requested) atoms. Cycle 3: After refmac, R = 0.2435 (Rfree = 0.000) for 3262 atoms. Found 12 (23 requested) and removed 17 (12 requested) atoms. Cycle 4: After refmac, R = 0.2366 (Rfree = 0.000) for 3248 atoms. Found 7 (23 requested) and removed 15 (12 requested) atoms. Cycle 5: After refmac, R = 0.2330 (Rfree = 0.000) for 3235 atoms. Found 3 (22 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 3.00 Search for helices and strands: 0 residues in 0 chains, 3367 seeds are put forward NCS extension: 33 residues added (4 deleted due to clashes), 3400 seeds are put forward Round 1: 316 peptides, 42 chains. Longest chain 24 peptides. Score 0.591 Round 2: 336 peptides, 39 chains. Longest chain 32 peptides. Score 0.658 Round 3: 342 peptides, 35 chains. Longest chain 28 peptides. Score 0.702 Round 4: 322 peptides, 38 chains. Longest chain 25 peptides. Score 0.640 Round 5: 335 peptides, 37 chains. Longest chain 26 peptides. Score 0.674 Taking the results from Round 3 Chains 37, Residues 307, Estimated correctness of the model 58.4 % 4 chains (61 residues) have been docked in sequence Building loops using Loopy2018 37 chains (307 residues) following loop building 4 chains (61 residues) in sequence following loop building ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6427 restraints for refining 3361 atoms. 4993 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2406 (Rfree = 0.000) for 3361 atoms. Found 20 (22 requested) and removed 25 (12 requested) atoms. Cycle 7: After refmac, R = 0.2217 (Rfree = 0.000) for 3327 atoms. Found 6 (22 requested) and removed 18 (12 requested) atoms. Cycle 8: After refmac, R = 0.2128 (Rfree = 0.000) for 3304 atoms. Found 6 (21 requested) and removed 15 (12 requested) atoms. Cycle 9: After refmac, R = 0.2072 (Rfree = 0.000) for 3287 atoms. Found 5 (20 requested) and removed 14 (12 requested) atoms. Cycle 10: After refmac, R = 0.2012 (Rfree = 0.000) for 3273 atoms. Found 5 (20 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.00 Search for helices and strands: 0 residues in 0 chains, 3354 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 3374 seeds are put forward Round 1: 322 peptides, 42 chains. Longest chain 21 peptides. Score 0.603 Round 2: 323 peptides, 38 chains. Longest chain 19 peptides. Score 0.642 Round 3: 338 peptides, 39 chains. Longest chain 36 peptides. Score 0.662 Round 4: 340 peptides, 36 chains. Longest chain 26 peptides. Score 0.691 Round 5: 345 peptides, 35 chains. Longest chain 45 peptides. Score 0.707 Taking the results from Round 5 Chains 39, Residues 310, Estimated correctness of the model 59.7 % 3 chains (76 residues) have been docked in sequence Building loops using Loopy2018 39 chains (310 residues) following loop building 3 chains (76 residues) in sequence following loop building ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6241 restraints for refining 3360 atoms. 4747 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2369 (Rfree = 0.000) for 3360 atoms. Found 11 (20 requested) and removed 36 (12 requested) atoms. Cycle 12: After refmac, R = 0.2196 (Rfree = 0.000) for 3318 atoms. Found 5 (19 requested) and removed 19 (12 requested) atoms. Cycle 13: After refmac, R = 0.2148 (Rfree = 0.000) for 3295 atoms. Found 6 (18 requested) and removed 20 (12 requested) atoms. Cycle 14: After refmac, R = 0.2070 (Rfree = 0.000) for 3272 atoms. Found 10 (18 requested) and removed 14 (12 requested) atoms. Cycle 15: After refmac, R = 0.2017 (Rfree = 0.000) for 3260 atoms. Found 4 (17 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.02 Search for helices and strands: 0 residues in 0 chains, 3324 seeds are put forward NCS extension: 34 residues added (31 deleted due to clashes), 3358 seeds are put forward Round 1: 308 peptides, 43 chains. Longest chain 22 peptides. Score 0.563 Round 2: 331 peptides, 39 chains. Longest chain 31 peptides. Score 0.649 Round 3: 325 peptides, 40 chains. Longest chain 24 peptides. Score 0.628 Round 4: 321 peptides, 38 chains. Longest chain 27 peptides. Score 0.638 Round 5: 331 peptides, 36 chains. Longest chain 26 peptides. Score 0.675 Taking the results from Round 5 Chains 39, Residues 295, Estimated correctness of the model 51.2 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 7010 restraints for refining 3361 atoms. 5780 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2415 (Rfree = 0.000) for 3361 atoms. Found 10 (17 requested) and removed 20 (12 requested) atoms. Cycle 17: After refmac, R = 0.2222 (Rfree = 0.000) for 3335 atoms. Found 6 (17 requested) and removed 14 (12 requested) atoms. Cycle 18: After refmac, R = 0.2173 (Rfree = 0.000) for 3323 atoms. Found 3 (17 requested) and removed 15 (12 requested) atoms. Cycle 19: After refmac, R = 0.2141 (Rfree = 0.000) for 3310 atoms. Found 5 (17 requested) and removed 17 (12 requested) atoms. Cycle 20: After refmac, R = 0.2217 (Rfree = 0.000) for 3298 atoms. Found 10 (17 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 2.97 Search for helices and strands: 0 residues in 0 chains, 3393 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 3412 seeds are put forward Round 1: 295 peptides, 44 chains. Longest chain 21 peptides. Score 0.522 Round 2: 300 peptides, 32 chains. Longest chain 31 peptides. Score 0.651 Round 3: 318 peptides, 37 chains. Longest chain 23 peptides. Score 0.641 Round 4: 312 peptides, 37 chains. Longest chain 29 peptides. Score 0.629 Round 5: 295 peptides, 31 chains. Longest chain 22 peptides. Score 0.651 Taking the results from Round 5 Chains 32, Residues 264, Estimated correctness of the model 44.4 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 7236 restraints for refining 3360 atoms. 6169 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2259 (Rfree = 0.000) for 3360 atoms. Found 6 (17 requested) and removed 19 (12 requested) atoms. Cycle 22: After refmac, R = 0.2099 (Rfree = 0.000) for 3340 atoms. Found 4 (17 requested) and removed 12 (12 requested) atoms. Cycle 23: After refmac, R = 0.2081 (Rfree = 0.000) for 3326 atoms. Found 6 (17 requested) and removed 14 (12 requested) atoms. Cycle 24: After refmac, R = 0.2029 (Rfree = 0.000) for 3318 atoms. Found 3 (17 requested) and removed 13 (12 requested) atoms. Cycle 25: After refmac, R = 0.2075 (Rfree = 0.000) for 3308 atoms. Found 7 (17 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 2.97 Search for helices and strands: 0 residues in 0 chains, 3398 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3422 seeds are put forward Round 1: 274 peptides, 41 chains. Longest chain 19 peptides. Score 0.502 Round 2: 302 peptides, 36 chains. Longest chain 30 peptides. Score 0.618 Round 3: 278 peptides, 33 chains. Longest chain 24 peptides. Score 0.596 Round 4: 301 peptides, 34 chains. Longest chain 24 peptides. Score 0.635 Round 5: 300 peptides, 38 chains. Longest chain 23 peptides. Score 0.595 Taking the results from Round 4 Chains 38, Residues 267, Estimated correctness of the model 39.7 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 7180 restraints for refining 3361 atoms. 6063 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2224 (Rfree = 0.000) for 3361 atoms. Found 14 (17 requested) and removed 18 (12 requested) atoms. Cycle 27: After refmac, R = 0.2084 (Rfree = 0.000) for 3351 atoms. Found 7 (17 requested) and removed 13 (12 requested) atoms. Cycle 28: After refmac, R = 0.2057 (Rfree = 0.000) for 3342 atoms. Found 5 (17 requested) and removed 12 (12 requested) atoms. Cycle 29: After refmac, R = 0.1979 (Rfree = 0.000) for 3333 atoms. Found 5 (17 requested) and removed 12 (12 requested) atoms. Cycle 30: After refmac, R = 0.1929 (Rfree = 0.000) for 3324 atoms. Found 2 (17 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 2.98 Search for helices and strands: 0 residues in 0 chains, 3413 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 3429 seeds are put forward Round 1: 264 peptides, 42 chains. Longest chain 22 peptides. Score 0.465 Round 2: 274 peptides, 37 chains. Longest chain 22 peptides. Score 0.546 Round 3: 304 peptides, 39 chains. Longest chain 23 peptides. Score 0.594 Round 4: 292 peptides, 36 chains. Longest chain 18 peptides. Score 0.597 Round 5: 294 peptides, 33 chains. Longest chain 27 peptides. Score 0.630 Taking the results from Round 5 Chains 34, Residues 261, Estimated correctness of the model 38.2 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 7101 restraints for refining 3361 atoms. 5970 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2327 (Rfree = 0.000) for 3361 atoms. Found 17 (17 requested) and removed 25 (12 requested) atoms. Cycle 32: After refmac, R = 0.2070 (Rfree = 0.000) for 3344 atoms. Found 12 (17 requested) and removed 18 (12 requested) atoms. Cycle 33: After refmac, R = 0.1979 (Rfree = 0.000) for 3328 atoms. Found 10 (17 requested) and removed 14 (12 requested) atoms. Cycle 34: After refmac, R = 0.2029 (Rfree = 0.000) for 3321 atoms. Found 4 (17 requested) and removed 16 (12 requested) atoms. Cycle 35: After refmac, R = 0.1899 (Rfree = 0.000) for 3302 atoms. Found 5 (17 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 2.96 Search for helices and strands: 0 residues in 0 chains, 3392 seeds are put forward NCS extension: 30 residues added (4 deleted due to clashes), 3422 seeds are put forward Round 1: 266 peptides, 40 chains. Longest chain 15 peptides. Score 0.493 Round 2: 278 peptides, 37 chains. Longest chain 15 peptides. Score 0.555 Round 3: 264 peptides, 34 chains. Longest chain 20 peptides. Score 0.554 Round 4: 285 peptides, 35 chains. Longest chain 19 peptides. Score 0.592 Round 5: 282 peptides, 33 chains. Longest chain 26 peptides. Score 0.605 Taking the results from Round 5 Chains 36, Residues 249, Estimated correctness of the model 30.3 % 5 chains (66 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6921 restraints for refining 3360 atoms. 5731 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2294 (Rfree = 0.000) for 3360 atoms. Found 16 (17 requested) and removed 34 (12 requested) atoms. Cycle 37: After refmac, R = 0.2080 (Rfree = 0.000) for 3336 atoms. Found 10 (17 requested) and removed 13 (12 requested) atoms. Cycle 38: After refmac, R = 0.1967 (Rfree = 0.000) for 3324 atoms. Found 3 (17 requested) and removed 14 (12 requested) atoms. Cycle 39: After refmac, R = 0.1931 (Rfree = 0.000) for 3308 atoms. Found 4 (17 requested) and removed 13 (12 requested) atoms. Cycle 40: After refmac, R = 0.1933 (Rfree = 0.000) for 3296 atoms. Found 1 (17 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 2.98 Search for helices and strands: 0 residues in 0 chains, 3363 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3380 seeds are put forward Round 1: 248 peptides, 39 chains. Longest chain 21 peptides. Score 0.457 Round 2: 269 peptides, 38 chains. Longest chain 32 peptides. Score 0.523 Round 3: 275 peptides, 40 chains. Longest chain 27 peptides. Score 0.516 Round 4: 279 peptides, 38 chains. Longest chain 32 peptides. Score 0.547 Round 5: 266 peptides, 37 chains. Longest chain 16 peptides. Score 0.526 Taking the results from Round 4 Chains 39, Residues 241, Estimated correctness of the model 10.4 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 7503 restraints for refining 3361 atoms. 6514 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2264 (Rfree = 0.000) for 3361 atoms. Found 13 (17 requested) and removed 26 (12 requested) atoms. Cycle 42: After refmac, R = 0.2115 (Rfree = 0.000) for 3345 atoms. Found 10 (17 requested) and removed 18 (12 requested) atoms. Cycle 43: After refmac, R = 0.2033 (Rfree = 0.000) for 3335 atoms. Found 8 (17 requested) and removed 19 (12 requested) atoms. Cycle 44: After refmac, R = 0.1982 (Rfree = 0.000) for 3318 atoms. Found 10 (17 requested) and removed 14 (12 requested) atoms. Cycle 45: After refmac, R = 0.1928 (Rfree = 0.000) for 3312 atoms. Found 3 (17 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.01 Search for helices and strands: 0 residues in 0 chains, 3383 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3402 seeds are put forward Round 1: 244 peptides, 42 chains. Longest chain 20 peptides. Score 0.410 Round 2: 243 peptides, 33 chains. Longest chain 21 peptides. Score 0.514 Round 3: 252 peptides, 33 chains. Longest chain 32 peptides. Score 0.536 Round 4: 236 peptides, 32 chains. Longest chain 25 peptides. Score 0.507 Round 5: 241 peptides, 34 chains. Longest chain 26 peptides. Score 0.497 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 219, Estimated correctness of the model 6.4 % 4 chains (25 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2otm-3_warpNtrace.pdb as input Building loops using Loopy2018 34 chains (219 residues) following loop building 4 chains (25 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7660 reflections ( 99.80 % complete ) and 7462 restraints for refining 3361 atoms. 6547 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2232 (Rfree = 0.000) for 3361 atoms. Found 0 (17 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2145 (Rfree = 0.000) for 3345 atoms. Found 0 (17 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2074 (Rfree = 0.000) for 3333 atoms. Found 0 (17 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.2052 (Rfree = 0.000) for 3318 atoms. TimeTaking 46.32