Mon 24 Dec 00:43:09 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 2pke-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pke-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pke-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-3.2-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/2pke-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-3.2-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 00:43:13 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/2pke-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-3.2-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 307 and 0 Target number of residues in the AU: 307 Target solvent content: 0.6303 Checking the provided sequence file Detected sequence length: 251 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 502 Adjusted target solvent content: 0.40 Input MTZ file: 2pke-3.2-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: 4 Cell parameters: 34.220 107.280 62.650 90.000 102.296 90.000 Input sequence file: 2pke-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4016 target number of atoms Had to go as low as 0.50 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: 61.213 3.200 Wilson plot Bfac: 66.17 7099 reflections ( 96.62 % complete ) and 0 restraints for refining 4450 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.2948 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2901 (Rfree = 0.000) for 4450 atoms. Found 39 (39 requested) and removed 132 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.64 Search for helices and strands: 0 residues in 0 chains, 4460 seeds are put forward NCS extension: 0 residues added, 4460 seeds are put forward Round 1: 189 peptides, 40 chains. Longest chain 9 peptides. Score 0.284 Round 2: 235 peptides, 41 chains. Longest chain 14 peptides. Score 0.435 Round 3: 235 peptides, 37 chains. Longest chain 15 peptides. Score 0.491 Round 4: 257 peptides, 37 chains. Longest chain 16 peptides. Score 0.557 Round 5: 258 peptides, 34 chains. Longest chain 22 peptides. Score 0.596 Taking the results from Round 5 Chains 39, Residues 224, Estimated correctness of the model 40.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8161 restraints for refining 3665 atoms. 7214 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2495 (Rfree = 0.000) for 3665 atoms. Found 23 (32 requested) and removed 38 (16 requested) atoms. Cycle 2: After refmac, R = 0.2317 (Rfree = 0.000) for 3626 atoms. Found 27 (32 requested) and removed 34 (16 requested) atoms. Cycle 3: After refmac, R = 0.2692 (Rfree = 0.000) for 3602 atoms. Found 32 (32 requested) and removed 43 (16 requested) atoms. Cycle 4: After refmac, R = 0.2494 (Rfree = 0.000) for 3553 atoms. Found 32 (32 requested) and removed 25 (16 requested) atoms. Cycle 5: After refmac, R = 0.2134 (Rfree = 0.000) for 3544 atoms. Found 16 (31 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 3.59 Search for helices and strands: 0 residues in 0 chains, 3702 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3718 seeds are put forward Round 1: 217 peptides, 41 chains. Longest chain 13 peptides. Score 0.373 Round 2: 260 peptides, 43 chains. Longest chain 15 peptides. Score 0.488 Round 3: 268 peptides, 42 chains. Longest chain 17 peptides. Score 0.526 Round 4: 280 peptides, 37 chains. Longest chain 18 peptides. Score 0.618 Round 5: 272 peptides, 37 chains. Longest chain 18 peptides. Score 0.598 Taking the results from Round 4 Chains 37, Residues 243, Estimated correctness of the model 45.8 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 7914 restraints for refining 3660 atoms. 6848 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2588 (Rfree = 0.000) for 3660 atoms. Found 23 (32 requested) and removed 44 (16 requested) atoms. Cycle 7: After refmac, R = 0.2407 (Rfree = 0.000) for 3615 atoms. Found 27 (32 requested) and removed 28 (16 requested) atoms. Cycle 8: After refmac, R = 0.2193 (Rfree = 0.000) for 3604 atoms. Found 21 (32 requested) and removed 22 (16 requested) atoms. Cycle 9: After refmac, R = 0.2388 (Rfree = 0.000) for 3598 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. Cycle 10: After refmac, R = 0.2215 (Rfree = 0.000) for 3599 atoms. Found 25 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 3.59 Search for helices and strands: 0 residues in 0 chains, 3746 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3767 seeds are put forward Round 1: 232 peptides, 39 chains. Longest chain 17 peptides. Score 0.454 Round 2: 255 peptides, 39 chains. Longest chain 21 peptides. Score 0.525 Round 3: 257 peptides, 36 chains. Longest chain 23 peptides. Score 0.569 Round 4: 270 peptides, 39 chains. Longest chain 19 peptides. Score 0.568 Round 5: 262 peptides, 36 chains. Longest chain 23 peptides. Score 0.583 Taking the results from Round 5 Chains 39, Residues 226, Estimated correctness of the model 36.4 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8198 restraints for refining 3665 atoms. 7221 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2376 (Rfree = 0.000) for 3665 atoms. Found 22 (32 requested) and removed 31 (16 requested) atoms. Cycle 12: After refmac, R = 0.2138 (Rfree = 0.000) for 3639 atoms. Found 21 (32 requested) and removed 24 (16 requested) atoms. Cycle 13: After refmac, R = 0.2128 (Rfree = 0.000) for 3630 atoms. Found 21 (32 requested) and removed 21 (16 requested) atoms. Cycle 14: After refmac, R = 0.2015 (Rfree = 0.000) for 3622 atoms. Found 21 (32 requested) and removed 19 (16 requested) atoms. Cycle 15: After refmac, R = 0.2070 (Rfree = 0.000) for 3619 atoms. Found 29 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.05 3.49 Search for helices and strands: 0 residues in 0 chains, 3761 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3782 seeds are put forward Round 1: 203 peptides, 39 chains. Longest chain 12 peptides. Score 0.353 Round 2: 231 peptides, 34 chains. Longest chain 19 peptides. Score 0.519 Round 3: 238 peptides, 36 chains. Longest chain 16 peptides. Score 0.514 Round 4: 242 peptides, 38 chains. Longest chain 24 peptides. Score 0.499 Round 5: 235 peptides, 38 chains. Longest chain 15 peptides. Score 0.477 Taking the results from Round 2 Chains 34, Residues 197, Estimated correctness of the model 17.4 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8441 restraints for refining 3664 atoms. 7614 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2086 (Rfree = 0.000) for 3664 atoms. Found 16 (32 requested) and removed 22 (16 requested) atoms. Cycle 17: After refmac, R = 0.2114 (Rfree = 0.000) for 3649 atoms. Found 22 (32 requested) and removed 21 (16 requested) atoms. Cycle 18: After refmac, R = 0.2072 (Rfree = 0.000) for 3644 atoms. Found 31 (32 requested) and removed 16 (16 requested) atoms. Cycle 19: After refmac, R = 0.2117 (Rfree = 0.000) for 3655 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. Cycle 20: After refmac, R = 0.1793 (Rfree = 0.000) for 3660 atoms. Found 7 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 3.57 Search for helices and strands: 0 residues in 0 chains, 3784 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3804 seeds are put forward Round 1: 196 peptides, 38 chains. Longest chain 11 peptides. Score 0.342 Round 2: 225 peptides, 35 chains. Longest chain 23 peptides. Score 0.487 Round 3: 227 peptides, 36 chains. Longest chain 19 peptides. Score 0.479 Round 4: 246 peptides, 37 chains. Longest chain 19 peptides. Score 0.525 Round 5: 224 peptides, 37 chains. Longest chain 17 peptides. Score 0.455 Taking the results from Round 4 Chains 39, Residues 209, Estimated correctness of the model 19.3 % 4 chains (46 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 7974 restraints for refining 3666 atoms. 7030 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2137 (Rfree = 0.000) for 3666 atoms. Found 17 (32 requested) and removed 24 (16 requested) atoms. Cycle 22: After refmac, R = 0.2218 (Rfree = 0.000) for 3647 atoms. Found 26 (32 requested) and removed 26 (16 requested) atoms. Cycle 23: After refmac, R = 0.2042 (Rfree = 0.000) for 3633 atoms. Found 18 (32 requested) and removed 17 (16 requested) atoms. Cycle 24: After refmac, R = 0.2159 (Rfree = 0.000) for 3631 atoms. Found 29 (32 requested) and removed 22 (16 requested) atoms. Cycle 25: After refmac, R = 0.2392 (Rfree = 0.000) for 3634 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 3.59 Search for helices and strands: 0 residues in 0 chains, 3780 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3802 seeds are put forward Round 1: 166 peptides, 28 chains. Longest chain 16 peptides. Score 0.389 Round 2: 192 peptides, 29 chains. Longest chain 20 peptides. Score 0.465 Round 3: 194 peptides, 31 chains. Longest chain 17 peptides. Score 0.442 Round 4: 201 peptides, 30 chains. Longest chain 16 peptides. Score 0.480 Round 5: 195 peptides, 30 chains. Longest chain 14 peptides. Score 0.460 Taking the results from Round 4 Chains 30, Residues 171, Estimated correctness of the model 4.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8617 restraints for refining 3629 atoms. 7963 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2564 (Rfree = 0.000) for 3629 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 27: After refmac, R = 0.2295 (Rfree = 0.000) for 3629 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 28: After refmac, R = 0.2374 (Rfree = 0.000) for 3630 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 29: After refmac, R = 0.2147 (Rfree = 0.000) for 3631 atoms. Found 32 (32 requested) and removed 18 (16 requested) atoms. Cycle 30: After refmac, R = 0.2166 (Rfree = 0.000) for 3642 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.09 3.54 Search for helices and strands: 0 residues in 0 chains, 3786 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3813 seeds are put forward Round 1: 167 peptides, 32 chains. Longest chain 11 peptides. Score 0.329 Round 2: 186 peptides, 32 chains. Longest chain 16 peptides. Score 0.399 Round 3: 192 peptides, 33 chains. Longest chain 13 peptides. Score 0.405 Round 4: 196 peptides, 31 chains. Longest chain 16 peptides. Score 0.449 Round 5: 186 peptides, 29 chains. Longest chain 16 peptides. Score 0.445 Taking the results from Round 4 Chains 31, Residues 165, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8571 restraints for refining 3666 atoms. 7903 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2534 (Rfree = 0.000) for 3666 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. Cycle 32: After refmac, R = 0.2237 (Rfree = 0.000) for 3673 atoms. Found 33 (33 requested) and removed 20 (16 requested) atoms. Cycle 33: After refmac, R = 0.2042 (Rfree = 0.000) for 3677 atoms. Found 21 (33 requested) and removed 91 (16 requested) atoms. Cycle 34: After refmac, R = 0.2283 (Rfree = 0.000) for 3605 atoms. Found 32 (32 requested) and removed 52 (16 requested) atoms. Cycle 35: After refmac, R = 0.2016 (Rfree = 0.000) for 3579 atoms. Found 32 (32 requested) and removed 36 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 3.58 Search for helices and strands: 0 residues in 0 chains, 3677 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3704 seeds are put forward Round 1: 142 peptides, 30 chains. Longest chain 10 peptides. Score 0.262 Round 2: 159 peptides, 31 chains. Longest chain 10 peptides. Score 0.314 Round 3: 172 peptides, 30 chains. Longest chain 11 peptides. Score 0.380 Round 4: 182 peptides, 32 chains. Longest chain 13 peptides. Score 0.385 Round 5: 176 peptides, 29 chains. Longest chain 13 peptides. Score 0.410 Taking the results from Round 5 Chains 29, Residues 147, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8479 restraints for refining 3625 atoms. 7873 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1991 (Rfree = 0.000) for 3625 atoms. Found 20 (32 requested) and removed 23 (16 requested) atoms. Cycle 37: After refmac, R = 0.2124 (Rfree = 0.000) for 3612 atoms. Found 32 (32 requested) and removed 21 (16 requested) atoms. Cycle 38: After refmac, R = 0.1995 (Rfree = 0.000) for 3620 atoms. Found 32 (32 requested) and removed 17 (16 requested) atoms. Cycle 39: After refmac, R = 0.1692 (Rfree = 0.000) for 3628 atoms. Found 7 (32 requested) and removed 16 (16 requested) atoms. Cycle 40: After refmac, R = 0.1970 (Rfree = 0.000) for 3612 atoms. Found 32 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 3.57 Search for helices and strands: 0 residues in 0 chains, 3752 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3767 seeds are put forward Round 1: 142 peptides, 30 chains. Longest chain 8 peptides. Score 0.262 Round 2: 143 peptides, 24 chains. Longest chain 13 peptides. Score 0.369 Round 3: 146 peptides, 25 chains. Longest chain 14 peptides. Score 0.364 Round 4: 153 peptides, 23 chains. Longest chain 14 peptides. Score 0.422 Round 5: 150 peptides, 26 chains. Longest chain 13 peptides. Score 0.362 Taking the results from Round 4 Chains 24, Residues 130, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8401 restraints for refining 3557 atoms. 7870 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2324 (Rfree = 0.000) for 3557 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Cycle 42: After refmac, R = 0.2645 (Rfree = 0.000) for 3560 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 43: After refmac, R = 0.2151 (Rfree = 0.000) for 3558 atoms. Found 31 (31 requested) and removed 16 (15 requested) atoms. Cycle 44: After refmac, R = 0.1996 (Rfree = 0.000) for 3570 atoms. Found 32 (32 requested) and removed 53 (16 requested) atoms. Cycle 45: After refmac, R = 0.1723 (Rfree = 0.000) for 3547 atoms. Found 22 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.07 3.51 Search for helices and strands: 0 residues in 0 chains, 3680 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3699 seeds are put forward Round 1: 105 peptides, 21 chains. Longest chain 11 peptides. Score 0.267 Round 2: 128 peptides, 24 chains. Longest chain 11 peptides. Score 0.310 Round 3: 137 peptides, 24 chains. Longest chain 12 peptides. Score 0.346 Round 4: 127 peptides, 22 chains. Longest chain 12 peptides. Score 0.341 Round 5: 133 peptides, 24 chains. Longest chain 14 peptides. Score 0.330 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 113, 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 2pke-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7099 reflections ( 96.62 % complete ) and 8321 restraints for refining 3508 atoms. 7893 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1868 (Rfree = 0.000) for 3508 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.1923 (Rfree = 0.000) for 3492 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1820 (Rfree = 0.000) for 3471 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1703 (Rfree = 0.000) for 3455 atoms. TimeTaking 38.47