Sun 23 Dec 22:22:42 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 2gb5-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gb5-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gb5-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-4.0-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/2gb5-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-4.0-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 22:23:43 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/2gb5-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-4.0-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 367 and 0 Target number of residues in the AU: 367 Target solvent content: 0.6627 Checking the provided sequence file Detected sequence length: 269 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 538 Adjusted target solvent content: 0.51 Input MTZ file: 2gb5-4.0-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: 18 Cell parameters: 99.287 103.553 57.270 90.000 90.000 90.000 Input sequence file: 2gb5-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 4304 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: 49.644 4.000 Wilson plot Bfac: 86.93 5306 reflections ( 99.23 % complete ) and 0 restraints for refining 4742 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3544 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3469 (Rfree = 0.000) for 4742 atoms. Found 9 (22 requested) and removed 28 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.82 3.77 Search for helices and strands: 0 residues in 0 chains, 4762 seeds are put forward NCS extension: 0 residues added, 4762 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 7 peptides. Score 0.229 Round 2: 122 peptides, 25 chains. Longest chain 12 peptides. Score 0.250 Round 3: 154 peptides, 30 chains. Longest chain 12 peptides. Score 0.286 Round 4: 159 peptides, 31 chains. Longest chain 10 peptides. Score 0.288 Round 5: 177 peptides, 34 chains. Longest chain 9 peptides. Score 0.304 Taking the results from Round 5 Chains 34, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 9685 restraints for refining 3887 atoms. 9147 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3247 (Rfree = 0.000) for 3887 atoms. Found 7 (18 requested) and removed 38 (9 requested) atoms. Cycle 2: After refmac, R = 0.3274 (Rfree = 0.000) for 3790 atoms. Found 13 (18 requested) and removed 27 (9 requested) atoms. Cycle 3: After refmac, R = 0.3148 (Rfree = 0.000) for 3740 atoms. Found 4 (17 requested) and removed 26 (8 requested) atoms. Cycle 4: After refmac, R = 0.3094 (Rfree = 0.000) for 3686 atoms. Found 6 (17 requested) and removed 19 (8 requested) atoms. Cycle 5: After refmac, R = 0.3004 (Rfree = 0.000) for 3638 atoms. Found 8 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.65 Search for helices and strands: 0 residues in 0 chains, 3703 seeds are put forward NCS extension: 0 residues added, 3703 seeds are put forward Round 1: 123 peptides, 28 chains. Longest chain 7 peptides. Score 0.208 Round 2: 163 peptides, 34 chains. Longest chain 8 peptides. Score 0.260 Round 3: 173 peptides, 36 chains. Longest chain 8 peptides. Score 0.265 Round 4: 184 peptides, 38 chains. Longest chain 9 peptides. Score 0.273 Round 5: 184 peptides, 36 chains. Longest chain 9 peptides. Score 0.300 Taking the results from Round 5 Chains 36, Residues 148, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 7328 restraints for refining 3256 atoms. 6690 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3025 (Rfree = 0.000) for 3256 atoms. Found 15 (15 requested) and removed 27 (7 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2897 (Rfree = 0.000) for 3216 atoms. Found 15 (15 requested) and removed 25 (7 requested) atoms. Cycle 8: After refmac, R = 0.2749 (Rfree = 0.000) for 3183 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 9: After refmac, R = 0.2665 (Rfree = 0.000) for 3175 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 10: After refmac, R = 0.2214 (Rfree = 0.000) for 3169 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 3.72 Search for helices and strands: 0 residues in 0 chains, 3259 seeds are put forward NCS extension: 0 residues added, 3259 seeds are put forward Round 1: 207 peptides, 42 chains. Longest chain 10 peptides. Score 0.292 Round 2: 222 peptides, 38 chains. Longest chain 16 peptides. Score 0.386 Round 3: 220 peptides, 37 chains. Longest chain 21 peptides. Score 0.392 Round 4: 235 peptides, 40 chains. Longest chain 16 peptides. Score 0.398 Round 5: 223 peptides, 36 chains. Longest chain 20 peptides. Score 0.413 Taking the results from Round 5 Chains 37, Residues 187, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 7707 restraints for refining 3442 atoms. 6921 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2667 (Rfree = 0.000) for 3442 atoms. Found 14 (16 requested) and removed 23 (8 requested) atoms. Cycle 12: After refmac, R = 0.2593 (Rfree = 0.000) for 3400 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 13: After refmac, R = 0.2103 (Rfree = 0.000) for 3379 atoms. Found 6 (16 requested) and removed 16 (8 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2082 (Rfree = 0.000) for 3359 atoms. Found 6 (16 requested) and removed 14 (8 requested) atoms. Cycle 15: After refmac, R = 0.1875 (Rfree = 0.000) for 3342 atoms. Found 5 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.66 Search for helices and strands: 0 residues in 0 chains, 3402 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3417 seeds are put forward Round 1: 205 peptides, 39 chains. Longest chain 11 peptides. Score 0.324 Round 2: 220 peptides, 38 chains. Longest chain 14 peptides. Score 0.380 Round 3: 226 peptides, 36 chains. Longest chain 13 peptides. Score 0.421 Round 4: 239 peptides, 39 chains. Longest chain 15 peptides. Score 0.421 Round 5: 211 peptides, 35 chains. Longest chain 11 peptides. Score 0.392 Taking the results from Round 4 Chains 39, Residues 200, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 8156 restraints for refining 3646 atoms. 7368 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2436 (Rfree = 0.000) for 3646 atoms. Found 17 (17 requested) and removed 33 (8 requested) atoms. Cycle 17: After refmac, R = 0.2241 (Rfree = 0.000) for 3599 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2188 (Rfree = 0.000) for 3573 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 19: After refmac, R = 0.1797 (Rfree = 0.000) for 3547 atoms. Found 7 (16 requested) and removed 9 (8 requested) atoms. Cycle 20: After refmac, R = 0.1728 (Rfree = 0.000) for 3532 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.68 Search for helices and strands: 0 residues in 0 chains, 3608 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3633 seeds are put forward Round 1: 160 peptides, 33 chains. Longest chain 8 peptides. Score 0.264 Round 2: 179 peptides, 31 chains. Longest chain 12 peptides. Score 0.350 Round 3: 180 peptides, 32 chains. Longest chain 13 peptides. Score 0.340 Round 4: 203 peptides, 35 chains. Longest chain 10 peptides. Score 0.369 Round 5: 208 peptides, 36 chains. Longest chain 18 peptides. Score 0.371 Taking the results from Round 5 Chains 36, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 8508 restraints for refining 3633 atoms. 7856 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2398 (Rfree = 0.000) for 3633 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 22: After refmac, R = 0.2218 (Rfree = 0.000) for 3601 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 23: After refmac, R = 0.2202 (Rfree = 0.000) for 3576 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 24: After refmac, R = 0.1822 (Rfree = 0.000) for 3550 atoms. Found 4 (16 requested) and removed 11 (8 requested) atoms. Cycle 25: After refmac, R = 0.1675 (Rfree = 0.000) for 3535 atoms. Found 1 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 3.69 Search for helices and strands: 0 residues in 0 chains, 3616 seeds are put forward NCS extension: 40 residues added (0 deleted due to clashes), 3656 seeds are put forward Round 1: 145 peptides, 31 chains. Longest chain 10 peptides. Score 0.242 Round 2: 193 peptides, 37 chains. Longest chain 10 peptides. Score 0.314 Round 3: 195 peptides, 37 chains. Longest chain 11 peptides. Score 0.320 Round 4: 203 peptides, 38 chains. Longest chain 11 peptides. Score 0.331 Round 5: 190 peptides, 34 chains. Longest chain 10 peptides. Score 0.344 Taking the results from Round 5 Chains 34, Residues 156, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 8369 restraints for refining 3612 atoms. 7735 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2395 (Rfree = 0.000) for 3612 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 27: After refmac, R = 0.2370 (Rfree = 0.000) for 3587 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 28: After refmac, R = 0.2104 (Rfree = 0.000) for 3567 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 29: After refmac, R = 0.1717 (Rfree = 0.000) for 3549 atoms. Found 0 (16 requested) and removed 15 (8 requested) atoms. Cycle 30: After refmac, R = 0.1633 (Rfree = 0.000) for 3527 atoms. Found 0 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 3.70 Search for helices and strands: 0 residues in 0 chains, 3597 seeds are put forward NCS extension: 5 residues added (1 deleted due to clashes), 3602 seeds are put forward Round 1: 171 peptides, 38 chains. Longest chain 7 peptides. Score 0.231 Round 2: 180 peptides, 36 chains. Longest chain 9 peptides. Score 0.287 Round 3: 200 peptides, 36 chains. Longest chain 17 peptides. Score 0.348 Round 4: 201 peptides, 36 chains. Longest chain 11 peptides. Score 0.351 Round 5: 205 peptides, 37 chains. Longest chain 15 peptides. Score 0.350 Taking the results from Round 4 Chains 36, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 8567 restraints for refining 3693 atoms. 7943 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2237 (Rfree = 0.000) for 3693 atoms. Found 14 (17 requested) and removed 28 (8 requested) atoms. Cycle 32: After refmac, R = 0.2287 (Rfree = 0.000) for 3660 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 33: After refmac, R = 0.2230 (Rfree = 0.000) for 3641 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 34: After refmac, R = 0.2163 (Rfree = 0.000) for 3630 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 35: After refmac, R = 0.2091 (Rfree = 0.000) for 3624 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.78 3.73 Search for helices and strands: 0 residues in 0 chains, 3739 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3750 seeds are put forward Round 1: 150 peptides, 32 chains. Longest chain 8 peptides. Score 0.245 Round 2: 162 peptides, 29 chains. Longest chain 10 peptides. Score 0.325 Round 3: 164 peptides, 28 chains. Longest chain 15 peptides. Score 0.345 Round 4: 164 peptides, 28 chains. Longest chain 12 peptides. Score 0.345 Round 5: 192 peptides, 31 chains. Longest chain 15 peptides. Score 0.388 Taking the results from Round 5 Chains 33, Residues 161, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 8657 restraints for refining 3743 atoms. 8016 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2293 (Rfree = 0.000) for 3743 atoms. Found 16 (17 requested) and removed 30 (8 requested) atoms. Cycle 37: After refmac, R = 0.2228 (Rfree = 0.000) for 3706 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 38: After refmac, R = 0.2147 (Rfree = 0.000) for 3685 atoms. Found 15 (17 requested) and removed 18 (8 requested) atoms. Cycle 39: After refmac, R = 0.1735 (Rfree = 0.000) for 3671 atoms. Found 2 (17 requested) and removed 14 (8 requested) atoms. Cycle 40: After refmac, R = 0.1683 (Rfree = 0.000) for 3644 atoms. Found 3 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.70 Search for helices and strands: 0 residues in 0 chains, 3705 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3719 seeds are put forward Round 1: 152 peptides, 33 chains. Longest chain 8 peptides. Score 0.237 Round 2: 181 peptides, 32 chains. Longest chain 13 peptides. Score 0.343 Round 3: 184 peptides, 33 chains. Longest chain 11 peptides. Score 0.339 Round 4: 176 peptides, 30 chains. Longest chain 10 peptides. Score 0.354 Round 5: 176 peptides, 32 chains. Longest chain 10 peptides. Score 0.328 Taking the results from Round 4 Chains 30, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 8815 restraints for refining 3735 atoms. 8261 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2211 (Rfree = 0.000) for 3735 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 42: After refmac, R = 0.2106 (Rfree = 0.000) for 3715 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 43: After refmac, R = 0.2042 (Rfree = 0.000) for 3702 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 44: After refmac, R = 0.2037 (Rfree = 0.000) for 3695 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 45: After refmac, R = 0.1571 (Rfree = 0.000) for 3689 atoms. Found 3 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.76 3.71 Search for helices and strands: 0 residues in 0 chains, 3766 seeds are put forward NCS extension: 0 residues added, 3766 seeds are put forward Round 1: 118 peptides, 26 chains. Longest chain 7 peptides. Score 0.221 Round 2: 135 peptides, 27 chains. Longest chain 10 peptides. Score 0.265 Round 3: 138 peptides, 24 chains. Longest chain 10 peptides. Score 0.319 Round 4: 123 peptides, 23 chains. Longest chain 10 peptides. Score 0.284 Round 5: 135 peptides, 24 chains. Longest chain 10 peptides. Score 0.309 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 114, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2gb5-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5306 reflections ( 99.23 % complete ) and 8420 restraints for refining 3636 atoms. 7955 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2042 (Rfree = 0.000) for 3636 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2174 (Rfree = 0.000) for 3616 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1920 (Rfree = 0.000) for 3601 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2017 (Rfree = 0.000) for 3583 atoms. TimeTaking 106.23