null Sun 23 Dec 22:23:05 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 2ghr-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ghr-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ghr-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-3.2-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/2ghr-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-3.2-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 22:23:15 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/2ghr-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-3.2-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 253 and 0 Target number of residues in the AU: 253 Target solvent content: 0.6042 Checking the provided sequence file Detected sequence length: 302 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 302 Adjusted target solvent content: 0.53 Input MTZ file: 2ghr-3.2-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: 91 Cell parameters: 95.828 95.828 75.339 90.000 90.000 90.000 Input sequence file: 2ghr-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2416 target number of atoms Had to go as low as 0.60 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 Loops will be built when appropriate and at the last cycle Resolution range: 95.828 3.200 Wilson plot Bfac: 54.20 6127 reflections ( 99.25 % complete ) and 0 restraints for refining 2700 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3388 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3107 (Rfree = 0.000) for 2700 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.02 2.90 Search for helices and strands: 0 residues in 0 chains, 2761 seeds are put forward Round 1: 139 peptides, 24 chains. Longest chain 17 peptides. Score 0.392 Round 2: 172 peptides, 23 chains. Longest chain 38 peptides. Score 0.551 Round 3: 184 peptides, 23 chains. Longest chain 19 peptides. Score 0.594 Round 4: 193 peptides, 21 chains. Longest chain 30 peptides. Score 0.654 Round 5: 188 peptides, 21 chains. Longest chain 24 peptides. Score 0.638 Taking the results from Round 4 Chains 21, Residues 172, Estimated correctness of the model 54.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6127 reflections ( 99.25 % complete ) and 4817 restraints for refining 2205 atoms. 4150 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2950 (Rfree = 0.000) for 2205 atoms. Found 18 (19 requested) and removed 17 (9 requested) atoms. Cycle 2: After refmac, R = 0.2719 (Rfree = 0.000) for 2174 atoms. Found 9 (19 requested) and removed 13 (9 requested) atoms. Cycle 3: After refmac, R = 0.2707 (Rfree = 0.000) for 2150 atoms. Found 6 (19 requested) and removed 11 (9 requested) atoms. Cycle 4: After refmac, R = 0.2676 (Rfree = 0.000) for 2139 atoms. Found 8 (19 requested) and removed 11 (9 requested) atoms. Cycle 5: After refmac, R = 0.2481 (Rfree = 0.000) for 2133 atoms. Found 7 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 2.91 Search for helices and strands: 0 residues in 0 chains, 2220 seeds are put forward Round 1: 153 peptides, 23 chains. Longest chain 15 peptides. Score 0.474 Round 2: 181 peptides, 24 chains. Longest chain 16 peptides. Score 0.567 Round 3: 199 peptides, 20 chains. Longest chain 16 peptides. Score 0.685 Round 4: 198 peptides, 25 chains. Longest chain 24 peptides. Score 0.611 Round 5: 216 peptides, 21 chains. Longest chain 33 peptides. Score 0.719 Taking the results from Round 5 Chains 22, Residues 195, Estimated correctness of the model 69.1 % 2 chains (16 residues) have been docked in sequence Building loops using Loopy2018 22 chains (195 residues) following loop building 2 chains (16 residues) in sequence following loop building ------------------------------------------------------ 6127 reflections ( 99.25 % complete ) and 4613 restraints for refining 2205 atoms. 3797 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2908 (Rfree = 0.000) for 2205 atoms. Found 14 (19 requested) and removed 13 (9 requested) atoms. Cycle 7: After refmac, R = 0.2801 (Rfree = 0.000) for 2195 atoms. Found 10 (19 requested) and removed 10 (9 requested) atoms. Cycle 8: After refmac, R = 0.2722 (Rfree = 0.000) for 2190 atoms. Found 7 (18 requested) and removed 10 (9 requested) atoms. Cycle 9: After refmac, R = 0.2715 (Rfree = 0.000) for 2185 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 10: After refmac, R = 0.2606 (Rfree = 0.000) for 2179 atoms. Found 2 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.00 2.88 Search for helices and strands: 0 residues in 0 chains, 2245 seeds are put forward Round 1: 182 peptides, 25 chains. Longest chain 26 peptides. Score 0.555 Round 2: 185 peptides, 21 chains. Longest chain 18 peptides. Score 0.628 Round 3: 191 peptides, 21 chains. Longest chain 20 peptides. Score 0.648 Round 4: 205 peptides, 21 chains. Longest chain 19 peptides. Score 0.689 Round 5: 215 peptides, 23 chains. Longest chain 21 peptides. Score 0.691 Taking the results from Round 5 Chains 23, Residues 192, Estimated correctness of the model 63.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6127 reflections ( 99.25 % complete ) and 4780 restraints for refining 2205 atoms. 4035 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2827 (Rfree = 0.000) for 2205 atoms. Found 17 (17 requested) and removed 13 (9 requested) atoms. Cycle 12: After refmac, R = 0.2682 (Rfree = 0.000) for 2191 atoms. Found 8 (17 requested) and removed 10 (9 requested) atoms. Cycle 13: After refmac, R = 0.2610 (Rfree = 0.000) for 2183 atoms. Found 5 (17 requested) and removed 10 (9 requested) atoms. Cycle 14: After refmac, R = 0.2555 (Rfree = 0.000) for 2176 atoms. Found 3 (17 requested) and removed 9 (9 requested) atoms. Cycle 15: After refmac, R = 0.2472 (Rfree = 0.000) for 2170 atoms. Found 0 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.07 2.95 Search for helices and strands: 0 residues in 0 chains, 2243 seeds are put forward Round 1: 181 peptides, 26 chains. Longest chain 17 peptides. Score 0.534 Round 2: 180 peptides, 20 chains. Longest chain 20 peptides. Score 0.627 Round 3: 195 peptides, 21 chains. Longest chain 21 peptides. Score 0.660 Round 4: 206 peptides, 23 chains. Longest chain 20 peptides. Score 0.665 Round 5: 204 peptides, 25 chains. Longest chain 21 peptides. Score 0.631 Taking the results from Round 4 Chains 23, Residues 183, Estimated correctness of the model 57.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6127 reflections ( 99.25 % complete ) and 4892 restraints for refining 2205 atoms. 4183 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3006 (Rfree = 0.000) for 2205 atoms. Found 17 (17 requested) and removed 13 (9 requested) atoms. Cycle 17: After refmac, R = 0.2628 (Rfree = 0.000) for 2208 atoms. Found 0 (17 requested) and removed 9 (9 requested) atoms. Cycle 18: After refmac, R = 0.2562 (Rfree = 0.000) for 2197 atoms. Found 2 (17 requested) and removed 9 (9 requested) atoms. Cycle 19: After refmac, R = 0.2527 (Rfree = 0.000) for 2189 atoms. Found 0 (17 requested) and removed 9 (9 requested) atoms. Cycle 20: After refmac, R = 0.2511 (Rfree = 0.000) for 2179 atoms. Found 0 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.05 2.93 Search for helices and strands: 0 residues in 0 chains, 2228 seeds are put forward Round 1: 184 peptides, 25 chains. Longest chain 24 peptides. Score 0.562 Round 2: 195 peptides, 23 chains. Longest chain 21 peptides. Score 0.631 Round 3: 190 peptides, 20 chains. Longest chain 28 peptides. Score 0.659 Round 4: 196 peptides, 22 chains. Longest chain 24 peptides. Score 0.649 Round 5: 197 peptides, 23 chains. Longest chain 25 peptides. Score 0.638 Taking the results from Round 3 Chains 22, Residues 170, Estimated correctness of the model 56.0 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6127 reflections ( 99.25 % complete ) and 4480 restraints for refining 2205 atoms. 3707 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2802 (Rfree = 0.000) for 2205 atoms. Found 17 (17 requested) and removed 14 (9 requested) atoms. Cycle 22: After refmac, R = 0.2574 (Rfree = 0.000) for 2203 atoms. Found 6 (17 requested) and removed 9 (9 requested) atoms. Cycle 23: After refmac, R = 0.2504 (Rfree = 0.000) for 2194 atoms. Found 2 (17 requested) and removed 10 (9 requested) atoms. Cycle 24: After refmac, R = 0.2468 (Rfree = 0.000) for 2184 atoms. Found 1 (17 requested) and removed 9 (9 requested) atoms. Cycle 25: After refmac, R = 0.2426 (Rfree = 0.000) for 2173 atoms. Found 2 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.06 2.94 Search for helices and strands: 0 residues in 0 chains, 2221 seeds are put forward Round 1: 171 peptides, 23 chains. Longest chain 23 peptides. Score 0.547 Round 2: 197 peptides, 20 chains. Longest chain 22 peptides. Score 0.680 Round 3: 194 peptides, 21 chains. Longest chain 29 peptides. Score 0.657 Round 4: 199 peptides, 22 chains. Longest chain 25 peptides. Score 0.658 Round 5: 207 peptides, 21 chains. Longest chain 26 peptides. Score 0.695 Taking the results from Round 5 Chains 21, Residues 186, Estimated correctness of the model 64.1 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6127 reflections ( 99.25 % complete ) and 4640 restraints for refining 2204 atoms. 3851 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2857 (Rfree = 0.000) for 2204 atoms. Found 15 (17 requested) and removed 10 (9 requested) atoms. Cycle 27: After refmac, R = 0.2638 (Rfree = 0.000) for 2204 atoms. Found 4 (17 requested) and removed 10 (9 requested) atoms. Cycle 28: After refmac, R = 0.2556 (Rfree = 0.000) for 2196 atoms. Found 7 (17 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.2519 (Rfree = 0.000) for 2190 atoms. Found 4 (17 requested) and removed 9 (9 requested) atoms. Cycle 30: After refmac, R = 0.2485 (Rfree = 0.000) for 2184 atoms. Found 1 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.05 2.93 Search for helices and strands: 0 residues in 0 chains, 2238 seeds are put forward Round 1: 183 peptides, 23 chains. Longest chain 25 peptides. Score 0.591 Round 2: 188 peptides, 19 chains. Longest chain 32 peptides. Score 0.667 Round 3: 191 peptides, 20 chains. Longest chain 27 peptides. Score 0.662 Round 4: 191 peptides, 20 chains. Longest chain 21 peptides. Score 0.662 Round 5: 192 peptides, 20 chains. Longest chain 26 peptides. Score 0.665 Taking the results from Round 2 Chains 20, Residues 169, Estimated correctness of the model 57.9 % 2 chains (39 residues) have been docked in sequence ------------------------------------------------------ 6127 reflections ( 99.25 % complete ) and 4506 restraints for refining 2205 atoms. 3687 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2878 (Rfree = 0.000) for 2205 atoms. Found 16 (17 requested) and removed 17 (9 requested) atoms. Cycle 32: After refmac, R = 0.2677 (Rfree = 0.000) for 2197 atoms. Found 8 (17 requested) and removed 10 (9 requested) atoms. Cycle 33: After refmac, R = 0.2580 (Rfree = 0.000) for 2193 atoms. Found 2 (17 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.2544 (Rfree = 0.000) for 2186 atoms. Found 1 (17 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.2527 (Rfree = 0.000) for 2178 atoms. Found 1 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.08 2.96 Search for helices and strands: 0 residues in 0 chains, 2233 seeds are put forward Round 1: 161 peptides, 22 chains. Longest chain 21 peptides. Score 0.525 Round 2: 178 peptides, 22 chains. Longest chain 19 peptides. Score 0.589 Round 3: 187 peptides, 21 chains. Longest chain 21 peptides. Score 0.635 Round 4: 185 peptides, 18 chains. Longest chain 29 peptides. Score 0.672 Round 5: 184 peptides, 16 chains. Longest chain 29 peptides. Score 0.697 Taking the results from Round 5 Chains 18, Residues 168, Estimated correctness of the model 64.5 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6127 reflections ( 99.25 % complete ) and 4750 restraints for refining 2205 atoms. 4006 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2798 (Rfree = 0.000) for 2205 atoms. Found 15 (17 requested) and removed 9 (9 requested) atoms. Cycle 37: After refmac, R = 0.2661 (Rfree = 0.000) for 2207 atoms. Found 9 (17 requested) and removed 9 (9 requested) atoms. Cycle 38: After refmac, R = 0.2575 (Rfree = 0.000) for 2205 atoms. Found 3 (17 requested) and removed 9 (9 requested) atoms. Cycle 39: After refmac, R = 0.2536 (Rfree = 0.000) for 2199 atoms. Found 1 (17 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.2533 (Rfree = 0.000) for 2190 atoms. Found 3 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.08 2.96 Search for helices and strands: 0 residues in 0 chains, 2231 seeds are put forward Round 1: 176 peptides, 24 chains. Longest chain 18 peptides. Score 0.549 Round 2: 184 peptides, 22 chains. Longest chain 21 peptides. Score 0.610 Round 3: 176 peptides, 20 chains. Longest chain 22 peptides. Score 0.614 Round 4: 167 peptides, 22 chains. Longest chain 15 peptides. Score 0.549 Round 5: 176 peptides, 23 chains. Longest chain 17 peptides. Score 0.566 Taking the results from Round 3 Chains 20, Residues 156, Estimated correctness of the model 44.8 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6127 reflections ( 99.25 % complete ) and 4751 restraints for refining 2205 atoms. 4038 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2833 (Rfree = 0.000) for 2205 atoms. Found 17 (17 requested) and removed 14 (9 requested) atoms. Cycle 42: After refmac, R = 0.2782 (Rfree = 0.000) for 2204 atoms. Found 10 (17 requested) and removed 9 (9 requested) atoms. Cycle 43: After refmac, R = 0.2719 (Rfree = 0.000) for 2201 atoms. Found 3 (17 requested) and removed 11 (9 requested) atoms. Cycle 44: After refmac, R = 0.2671 (Rfree = 0.000) for 2190 atoms. Found 7 (17 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.2592 (Rfree = 0.000) for 2186 atoms. Found 6 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.08 2.96 Search for helices and strands: 0 residues in 0 chains, 2237 seeds are put forward Round 1: 149 peptides, 25 chains. Longest chain 17 peptides. Score 0.418 Round 2: 149 peptides, 21 chains. Longest chain 20 peptides. Score 0.495 Round 3: 164 peptides, 22 chains. Longest chain 23 peptides. Score 0.537 Round 4: 170 peptides, 21 chains. Longest chain 20 peptides. Score 0.577 Round 5: 173 peptides, 21 chains. Longest chain 23 peptides. Score 0.587 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 152, Estimated correctness of the model 37.5 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2ghr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6127 reflections ( 99.25 % complete ) and 5032 restraints for refining 2205 atoms. 4445 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2795 (Rfree = 0.000) for 2205 atoms. Found 0 (17 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2701 (Rfree = 0.000) for 2191 atoms. Found 0 (17 requested) and removed 5 (9 requested) atoms. Cycle 48: After refmac, R = 0.2654 (Rfree = 0.000) for 2184 atoms. Found 0 (17 requested) and removed 1 (9 requested) atoms. Cycle 49: After refmac, R = 0.2600 (Rfree = 0.000) for 2183 atoms. Found 0 (17 requested) and removed 1 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:10:29 GMT 2018 Job finished. TimeTaking 47.4 Used memory is bytes: 429640