Mon 24 Dec 07:26:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fno-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fno-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fno-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.8-parrot-noncs ############### 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 07:27:00 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/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.8-parrot-noncs/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 379 and 0 Target number of residues in the AU: 379 Target solvent content: 0.6507 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-3.8-parrot-noncs.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-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3968 target number of atoms Had to go as low as 0.80 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 3.800 Wilson plot Bfac: 78.04 5866 reflections ( 99.07 % complete ) and 0 restraints for refining 4415 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3432 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3455 (Rfree = 0.000) for 4415 atoms. Found 24 (24 requested) and removed 42 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 3.46 Search for helices and strands: 0 residues in 0 chains, 4534 seeds are put forward NCS extension: 0 residues added, 4534 seeds are put forward Round 1: 184 peptides, 42 chains. Longest chain 6 peptides. Score 0.220 Round 2: 234 peptides, 43 chains. Longest chain 9 peptides. Score 0.360 Round 3: 248 peptides, 39 chains. Longest chain 11 peptides. Score 0.445 Round 4: 247 peptides, 37 chains. Longest chain 16 peptides. Score 0.465 Round 5: 253 peptides, 38 chains. Longest chain 13 peptides. Score 0.469 Taking the results from Round 5 Chains 38, Residues 215, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8427 restraints for refining 3588 atoms. 7605 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2806 (Rfree = 0.000) for 3588 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 2: After refmac, R = 0.2602 (Rfree = 0.000) for 3496 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 3: After refmac, R = 0.2550 (Rfree = 0.000) for 3452 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2481 (Rfree = 0.000) for 3423 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 5: After refmac, R = 0.2400 (Rfree = 0.000) for 3392 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.41 Search for helices and strands: 0 residues in 0 chains, 3570 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3583 seeds are put forward Round 1: 217 peptides, 41 chains. Longest chain 10 peptides. Score 0.335 Round 2: 251 peptides, 41 chains. Longest chain 11 peptides. Score 0.430 Round 3: 235 peptides, 35 chains. Longest chain 14 peptides. Score 0.457 Round 4: 235 peptides, 34 chains. Longest chain 14 peptides. Score 0.469 Round 5: 244 peptides, 36 chains. Longest chain 12 peptides. Score 0.469 Taking the results from Round 5 Chains 36, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8407 restraints for refining 3560 atoms. 7611 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2305 (Rfree = 0.000) for 3560 atoms. Found 19 (19 requested) and removed 34 (9 requested) atoms. Cycle 7: After refmac, R = 0.2379 (Rfree = 0.000) for 3521 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 8: After refmac, R = 0.2179 (Rfree = 0.000) for 3503 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 9: After refmac, R = 0.2188 (Rfree = 0.000) for 3498 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 10: After refmac, R = 0.2191 (Rfree = 0.000) for 3499 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 3675 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3686 seeds are put forward Round 1: 217 peptides, 42 chains. Longest chain 13 peptides. Score 0.323 Round 2: 238 peptides, 36 chains. Longest chain 17 peptides. Score 0.453 Round 3: 238 peptides, 38 chains. Longest chain 13 peptides. Score 0.430 Round 4: 242 peptides, 36 chains. Longest chain 21 peptides. Score 0.464 Round 5: 237 peptides, 31 chains. Longest chain 19 peptides. Score 0.507 Taking the results from Round 5 Chains 31, Residues 206, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8548 restraints for refining 3588 atoms. 7755 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2511 (Rfree = 0.000) for 3588 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 12: After refmac, R = 0.2411 (Rfree = 0.000) for 3565 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 13: After refmac, R = 0.2204 (Rfree = 0.000) for 3545 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 14: After refmac, R = 0.2299 (Rfree = 0.000) for 3539 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 15: After refmac, R = 0.2209 (Rfree = 0.000) for 3533 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.65 3.46 Search for helices and strands: 0 residues in 0 chains, 3682 seeds are put forward NCS extension: 0 residues added, 3682 seeds are put forward Round 1: 196 peptides, 38 chains. Longest chain 9 peptides. Score 0.311 Round 2: 230 peptides, 35 chains. Longest chain 12 peptides. Score 0.444 Round 3: 235 peptides, 34 chains. Longest chain 15 peptides. Score 0.469 Round 4: 236 peptides, 37 chains. Longest chain 20 peptides. Score 0.437 Round 5: 224 peptides, 32 chains. Longest chain 17 peptides. Score 0.463 Taking the results from Round 3 Chains 34, Residues 201, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8463 restraints for refining 3588 atoms. 7683 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2370 (Rfree = 0.000) for 3588 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 17: After refmac, R = 0.2397 (Rfree = 0.000) for 3561 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 18: After refmac, R = 0.2181 (Rfree = 0.000) for 3546 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 19: After refmac, R = 0.2241 (Rfree = 0.000) for 3531 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 20: After refmac, R = 0.1951 (Rfree = 0.000) for 3525 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.47 Search for helices and strands: 0 residues in 0 chains, 3671 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3688 seeds are put forward Round 1: 180 peptides, 36 chains. Longest chain 10 peptides. Score 0.287 Round 2: 206 peptides, 38 chains. Longest chain 14 peptides. Score 0.341 Round 3: 199 peptides, 34 chains. Longest chain 14 peptides. Score 0.371 Round 4: 213 peptides, 35 chains. Longest chain 15 peptides. Score 0.398 Round 5: 222 peptides, 35 chains. Longest chain 20 peptides. Score 0.423 Taking the results from Round 5 Chains 35, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8515 restraints for refining 3589 atoms. 7802 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2231 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 22: After refmac, R = 0.2202 (Rfree = 0.000) for 3563 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 23: After refmac, R = 0.2026 (Rfree = 0.000) for 3554 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 24: After refmac, R = 0.1986 (Rfree = 0.000) for 3540 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 25: After refmac, R = 0.1962 (Rfree = 0.000) for 3537 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.46 Search for helices and strands: 0 residues in 0 chains, 3685 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3704 seeds are put forward Round 1: 168 peptides, 32 chains. Longest chain 13 peptides. Score 0.303 Round 2: 178 peptides, 31 chains. Longest chain 14 peptides. Score 0.347 Round 3: 195 peptides, 35 chains. Longest chain 15 peptides. Score 0.346 Round 4: 209 peptides, 34 chains. Longest chain 15 peptides. Score 0.399 Round 5: 211 peptides, 33 chains. Longest chain 15 peptides. Score 0.417 Taking the results from Round 5 Chains 33, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8555 restraints for refining 3589 atoms. 7876 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2337 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 27: After refmac, R = 0.2149 (Rfree = 0.000) for 3569 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 28: After refmac, R = 0.2091 (Rfree = 0.000) for 3556 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 29: After refmac, R = 0.1998 (Rfree = 0.000) for 3555 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 30: After refmac, R = 0.1912 (Rfree = 0.000) for 3552 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 3729 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3747 seeds are put forward Round 1: 172 peptides, 34 chains. Longest chain 15 peptides. Score 0.289 Round 2: 193 peptides, 35 chains. Longest chain 15 peptides. Score 0.340 Round 3: 201 peptides, 32 chains. Longest chain 18 peptides. Score 0.401 Round 4: 203 peptides, 31 chains. Longest chain 17 peptides. Score 0.419 Round 5: 201 peptides, 32 chains. Longest chain 16 peptides. Score 0.401 Taking the results from Round 4 Chains 31, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8739 restraints for refining 3589 atoms. 8082 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2341 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 32: After refmac, R = 0.2466 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 33: After refmac, R = 0.2177 (Rfree = 0.000) for 3573 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 34: After refmac, R = 0.2407 (Rfree = 0.000) for 3565 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 35: After refmac, R = 0.2009 (Rfree = 0.000) for 3561 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.42 Search for helices and strands: 0 residues in 0 chains, 3661 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3677 seeds are put forward Round 1: 196 peptides, 43 chains. Longest chain 8 peptides. Score 0.246 Round 2: 202 peptides, 36 chains. Longest chain 13 peptides. Score 0.354 Round 3: 205 peptides, 36 chains. Longest chain 11 peptides. Score 0.363 Round 4: 208 peptides, 37 chains. Longest chain 10 peptides. Score 0.359 Round 5: 195 peptides, 34 chains. Longest chain 11 peptides. Score 0.359 Taking the results from Round 3 Chains 36, Residues 169, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8713 restraints for refining 3588 atoms. 8058 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2157 (Rfree = 0.000) for 3588 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 37: After refmac, R = 0.1965 (Rfree = 0.000) for 3579 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 38: After refmac, R = 0.2032 (Rfree = 0.000) for 3578 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 39: After refmac, R = 0.1850 (Rfree = 0.000) for 3576 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 40: After refmac, R = 0.1860 (Rfree = 0.000) for 3566 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.44 Search for helices and strands: 0 residues in 0 chains, 3686 seeds are put forward NCS extension: 9 residues added (1 deleted due to clashes), 3695 seeds are put forward Round 1: 164 peptides, 34 chains. Longest chain 8 peptides. Score 0.263 Round 2: 192 peptides, 35 chains. Longest chain 9 peptides. Score 0.337 Round 3: 202 peptides, 35 chains. Longest chain 10 peptides. Score 0.367 Round 4: 186 peptides, 33 chains. Longest chain 12 peptides. Score 0.345 Round 5: 176 peptides, 29 chains. Longest chain 10 peptides. Score 0.368 Taking the results from Round 5 Chains 29, Residues 147, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8856 restraints for refining 3587 atoms. 8297 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2156 (Rfree = 0.000) for 3587 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 42: After refmac, R = 0.1970 (Rfree = 0.000) for 3584 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 43: After refmac, R = 0.1924 (Rfree = 0.000) for 3587 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 44: After refmac, R = 0.1839 (Rfree = 0.000) for 3587 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 45: After refmac, R = 0.1517 (Rfree = 0.000) for 3589 atoms. Found 3 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 3668 seeds are put forward NCS extension: 0 residues added, 3668 seeds are put forward Round 1: 157 peptides, 32 chains. Longest chain 12 peptides. Score 0.268 Round 2: 182 peptides, 31 chains. Longest chain 12 peptides. Score 0.359 Round 3: 176 peptides, 29 chains. Longest chain 12 peptides. Score 0.368 Round 4: 174 peptides, 30 chains. Longest chain 12 peptides. Score 0.349 Round 5: 178 peptides, 29 chains. Longest chain 11 peptides. Score 0.374 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 149, 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 2fno-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5866 reflections ( 99.07 % complete ) and 8695 restraints for refining 3588 atoms. 8128 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2061 (Rfree = 0.000) for 3588 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2073 (Rfree = 0.000) for 3569 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2060 (Rfree = 0.000) for 3549 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1598 (Rfree = 0.000) for 3534 atoms. TimeTaking 41.2