Tue 25 Dec 19:27:57 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ghr-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ghr-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-3.6-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 ============================================================ Tue 25 Dec 19:28:07 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-3.6-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 251 and 0 Target number of residues in the AU: 251 Target solvent content: 0.6073 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-3.6-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-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2416 target number of atoms Had to go as low as 0.65 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 3.600 Wilson plot Bfac: 55.16 4349 reflections ( 98.95 % complete ) and 0 restraints for refining 2659 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3457 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3719 (Rfree = 0.000) for 2659 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.15 Search for helices and strands: 0 residues in 0 chains, 2701 seeds are put forward Round 1: 90 peptides, 17 chains. Longest chain 12 peptides. Score 0.298 Round 2: 134 peptides, 22 chains. Longest chain 13 peptides. Score 0.409 Round 3: 140 peptides, 23 chains. Longest chain 11 peptides. Score 0.417 Round 4: 153 peptides, 23 chains. Longest chain 13 peptides. Score 0.474 Round 5: 142 peptides, 21 chains. Longest chain 23 peptides. Score 0.465 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 ------------------------------------------------------ 4349 reflections ( 98.95 % complete ) and 4850 restraints for refining 2121 atoms. 4321 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3464 (Rfree = 0.000) for 2121 atoms. Found 9 (13 requested) and removed 14 (6 requested) atoms. Cycle 2: After refmac, R = 0.3248 (Rfree = 0.000) for 2064 atoms. Found 12 (13 requested) and removed 10 (6 requested) atoms. Cycle 3: After refmac, R = 0.3081 (Rfree = 0.000) for 2036 atoms. Found 10 (13 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.3085 (Rfree = 0.000) for 2015 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 5: After refmac, R = 0.3123 (Rfree = 0.000) for 1995 atoms. Found 9 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.05 Search for helices and strands: 0 residues in 0 chains, 2032 seeds are put forward Round 1: 140 peptides, 25 chains. Longest chain 10 peptides. Score 0.377 Round 2: 169 peptides, 24 chains. Longest chain 17 peptides. Score 0.522 Round 3: 161 peptides, 23 chains. Longest chain 12 peptides. Score 0.507 Round 4: 164 peptides, 21 chains. Longest chain 18 peptides. Score 0.554 Round 5: 175 peptides, 23 chains. Longest chain 17 peptides. Score 0.562 Taking the results from Round 5 Chains 23, Residues 152, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4349 reflections ( 98.95 % complete ) and 4624 restraints for refining 2084 atoms. 4021 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3708 (Rfree = 0.000) for 2084 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 7: After refmac, R = 0.3450 (Rfree = 0.000) for 2053 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 8: After refmac, R = 0.3340 (Rfree = 0.000) for 2026 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 9: After refmac, R = 0.3238 (Rfree = 0.000) for 1995 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.3087 (Rfree = 0.000) for 1986 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.06 Search for helices and strands: 0 residues in 0 chains, 2038 seeds are put forward Round 1: 138 peptides, 22 chains. Longest chain 21 peptides. Score 0.428 Round 2: 165 peptides, 25 chains. Longest chain 19 peptides. Score 0.488 Round 3: 167 peptides, 22 chains. Longest chain 19 peptides. Score 0.549 Round 4: 171 peptides, 23 chains. Longest chain 19 peptides. Score 0.547 Round 5: 166 peptides, 22 chains. Longest chain 19 peptides. Score 0.545 Taking the results from Round 3 Chains 22, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4349 reflections ( 98.95 % complete ) and 4391 restraints for refining 1990 atoms. 3833 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3233 (Rfree = 0.000) for 1990 atoms. Found 5 (12 requested) and removed 11 (6 requested) atoms. Cycle 12: After refmac, R = 0.3108 (Rfree = 0.000) for 1961 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2962 (Rfree = 0.000) for 1943 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.3059 (Rfree = 0.000) for 1935 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.2714 (Rfree = 0.000) for 1929 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 3.06 Search for helices and strands: 0 residues in 0 chains, 1959 seeds are put forward Round 1: 145 peptides, 25 chains. Longest chain 14 peptides. Score 0.400 Round 2: 156 peptides, 22 chains. Longest chain 16 peptides. Score 0.505 Round 3: 174 peptides, 25 chains. Longest chain 14 peptides. Score 0.524 Round 4: 169 peptides, 23 chains. Longest chain 13 peptides. Score 0.539 Round 5: 167 peptides, 25 chains. Longest chain 11 peptides. Score 0.496 Taking the results from Round 4 Chains 23, Residues 146, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4349 reflections ( 98.95 % complete ) and 4267 restraints for refining 2045 atoms. 3638 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3186 (Rfree = 0.000) for 2045 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 17: After refmac, R = 0.3041 (Rfree = 0.000) for 2021 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 18: After refmac, R = 0.2693 (Rfree = 0.000) for 2004 atoms. Found 7 (12 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.2836 (Rfree = 0.000) for 1995 atoms. Found 9 (12 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.2846 (Rfree = 0.000) for 1982 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.17 Search for helices and strands: 0 residues in 0 chains, 2054 seeds are put forward Round 1: 145 peptides, 24 chains. Longest chain 12 peptides. Score 0.420 Round 2: 156 peptides, 22 chains. Longest chain 15 peptides. Score 0.505 Round 3: 163 peptides, 24 chains. Longest chain 13 peptides. Score 0.498 Round 4: 171 peptides, 25 chains. Longest chain 15 peptides. Score 0.512 Round 5: 167 peptides, 24 chains. Longest chain 15 peptides. Score 0.514 Taking the results from Round 5 Chains 24, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4349 reflections ( 98.95 % complete ) and 4850 restraints for refining 2139 atoms. 4302 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3318 (Rfree = 0.000) for 2139 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 22: After refmac, R = 0.3231 (Rfree = 0.000) for 2098 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.3123 (Rfree = 0.000) for 2073 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.3021 (Rfree = 0.000) for 2055 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.2753 (Rfree = 0.000) for 2051 atoms. Found 11 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 3.06 Search for helices and strands: 0 residues in 0 chains, 2094 seeds are put forward Round 1: 128 peptides, 22 chains. Longest chain 12 peptides. Score 0.381 Round 2: 146 peptides, 20 chains. Longest chain 21 peptides. Score 0.501 Round 3: 157 peptides, 27 chains. Longest chain 13 peptides. Score 0.416 Round 4: 151 peptides, 24 chains. Longest chain 11 peptides. Score 0.447 Round 5: 154 peptides, 21 chains. Longest chain 14 peptides. Score 0.515 Taking the results from Round 5 Chains 22, Residues 133, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4349 reflections ( 98.95 % complete ) and 4812 restraints for refining 2172 atoms. 4268 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3524 (Rfree = 0.000) for 2172 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.3041 (Rfree = 0.000) for 2146 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 28: After refmac, R = 0.3118 (Rfree = 0.000) for 2139 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.3004 (Rfree = 0.000) for 2131 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.2956 (Rfree = 0.000) for 2130 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 3.02 Search for helices and strands: 0 residues in 0 chains, 2196 seeds are put forward Round 1: 122 peptides, 23 chains. Longest chain 8 peptides. Score 0.330 Round 2: 148 peptides, 24 chains. Longest chain 14 peptides. Score 0.433 Round 3: 135 peptides, 22 chains. Longest chain 15 peptides. Score 0.414 Round 4: 124 peptides, 21 chains. Longest chain 12 peptides. Score 0.383 Round 5: 139 peptides, 22 chains. Longest chain 15 peptides. Score 0.432 Taking the results from Round 2 Chains 24, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4349 reflections ( 98.95 % complete ) and 4855 restraints for refining 2142 atoms. 4383 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3033 (Rfree = 0.000) for 2142 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2783 (Rfree = 0.000) for 2123 atoms. Found 9 (13 requested) and removed 11 (6 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2624 (Rfree = 0.000) for 2113 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.2477 (Rfree = 0.000) for 2113 atoms. Found 11 (13 requested) and removed 8 (6 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2707 (Rfree = 0.000) for 2114 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.10 Search for helices and strands: 0 residues in 0 chains, 2156 seeds are put forward Round 1: 121 peptides, 26 chains. Longest chain 9 peptides. Score 0.260 Round 2: 131 peptides, 25 chains. Longest chain 13 peptides. Score 0.333 Round 3: 122 peptides, 21 chains. Longest chain 14 peptides. Score 0.373 Round 4: 133 peptides, 22 chains. Longest chain 14 peptides. Score 0.405 Round 5: 145 peptides, 24 chains. Longest chain 14 peptides. Score 0.420 Taking the results from Round 5 Chains 24, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4349 reflections ( 98.95 % complete ) and 4997 restraints for refining 2190 atoms. 4537 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3159 (Rfree = 0.000) for 2190 atoms. Found 14 (14 requested) and removed 26 (7 requested) atoms. Cycle 37: After refmac, R = 0.2798 (Rfree = 0.000) for 2160 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 38: After refmac, R = 0.2621 (Rfree = 0.000) for 2154 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 39: After refmac, R = 0.2262 (Rfree = 0.000) for 2150 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2152 (Rfree = 0.000) for 2148 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.09 2.97 Search for helices and strands: 0 residues in 0 chains, 2184 seeds are put forward Round 1: 105 peptides, 23 chains. Longest chain 9 peptides. Score 0.241 Round 2: 123 peptides, 22 chains. Longest chain 16 peptides. Score 0.357 Round 3: 129 peptides, 19 chains. Longest chain 16 peptides. Score 0.447 Round 4: 141 peptides, 25 chains. Longest chain 17 peptides. Score 0.381 Round 5: 135 peptides, 20 chains. Longest chain 16 peptides. Score 0.454 Taking the results from Round 5 Chains 20, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4349 reflections ( 98.95 % complete ) and 4908 restraints for refining 2190 atoms. 4468 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2859 (Rfree = 0.000) for 2190 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. Cycle 42: After refmac, R = 0.2761 (Rfree = 0.000) for 2179 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. Cycle 43: After refmac, R = 0.2599 (Rfree = 0.000) for 2175 atoms. Found 11 (14 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2706 (Rfree = 0.000) for 2175 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 45: After refmac, R = 0.2289 (Rfree = 0.000) for 2171 atoms. Found 7 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.06 Search for helices and strands: 0 residues in 0 chains, 2209 seeds are put forward Round 1: 100 peptides, 21 chains. Longest chain 17 peptides. Score 0.259 Round 2: 109 peptides, 20 chains. Longest chain 11 peptides. Score 0.330 Round 3: 109 peptides, 17 chains. Longest chain 17 peptides. Score 0.396 Round 4: 109 peptides, 20 chains. Longest chain 10 peptides. Score 0.330 Round 5: 109 peptides, 17 chains. Longest chain 14 peptides. Score 0.396 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 92, 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 2ghr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4349 reflections ( 98.95 % complete ) and 4981 restraints for refining 2175 atoms. 4630 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2712 (Rfree = 0.000) for 2175 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2710 (Rfree = 0.000) for 2164 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2456 (Rfree = 0.000) for 2156 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2154 (Rfree = 0.000) for 2149 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:12:59 GMT 2018 Job finished. TimeTaking 45.05